[gmx-users] genion causing atom to be in multiple T-Coupling groups (2024)

Discussion:

[gmx-users] genion causing atom to be in multiple T-Coupling groups

Una Bjarnadottir

2006-09-08 12:21:02 UTC

Permalink

Dear Users,

I'm trying to neutralize my system adding 3 Cl ions with genion and when
running grompp again with the new generated .gro file I get this error:
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1
are Cl and protein groups if I on the other hand do not neutralize the
system the run goes fine! So there is something wrong with how the
genion works for me. I followed the tutorial and chose the SOL group
and water molecules were replaced by the Cl ions. Than I modifyed the
.top file and took 3 sol molecules and added the 3 ions.
_*
*_Best regards for any help, Una Bjarnadottir
_*
.top before:
*_; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL 9719
_*.top after*_
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL 9716
CL- 3

_*These are my commands:*_
#
#Run grompp
#
emfile_mdpfile='em.mdp'
emout='em_out.mdp'
structure_file='em.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)

#
#Run genion
#
ion_out='ion.gro'
os.system('/usr/local/bin/genion -s '+structure_file+ ' -o '
+ion_out+ ' -nname Cl -nn 3')

#
#Run grompp
#
structure_file_after_genion='em_genion.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p '
+topologyfile)

Una Bjarnadottir

2006-09-11 11:00:00 UTC

Permalink

Dear Users,

I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When
running grompp after genion with the new generated .gro file I get this error:

Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1
are Cl and protein groups if I on the other hand do not neutralize the
system the run goes fine!
When looking into the .ndx file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other). How can I change the group definitions and make sure the groups do not overlap and to be unique?

It seems to be something wrong with how the genion works for me. I followed the tutorial and chose the SOL group
and water molecules were replaced by the Cl ions. Than I modifyed the
.top file and took 3 sol molecules and added the 3 ions.

Please help because have not been able to fix the problem with related letters on the subject on the list.

Best regards, Una Bjarnadottir

.top before:
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL 9719

.top after
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL 9716
CL- 3

These are my commands:
#
#Run grompp
#
emfile_mdpfile='em.mdp'
emout='em_out.mdp'
structure_file='em.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)

#
#Run genion
#
ion_out='ion.gro'
os.system('/usr/local/bin/genion -s '+structure_file+ ' -o '
+ion_out+ ' -nname Cl -nn 3')

#
#Run grompp
#
structure_file_after_genion='em_genion.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p '
+topologyfile)

David van der Spoel

2006-09-11 12:22:22 UTC

Permalink

Post by Una Bjarnadottir
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system
adding 3 Cl ions with genion. When running grompp after genion with the
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
which is the last water atom (total in system 33003) and groups 15 and 1
are Cl and protein groups if I on the other hand do not neutralize the
system the run goes fine! When looking into the .ndx file atom 33000 is
in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other).
How can I change the group definitions and make sure the groups do not
overlap and to be unique?
It seems to be something wrong with how the genion works for me. I
followed the tutorial and chose the SOL group and water molecules were
replaced by the Cl ions. Than I modifyed the .top file and took 3 sol
molecules and added the 3 ions.
Please help because have not been able to fix the problem with related
letters on the subject on the list.
Best regards, Una Bjarnadottir

What do your tcoupl groups look like?

Could it be System SOL?

The number may be confusing, you should subtract one from them when
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T
coupling group.

--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:46 18 471 4205fax: 46 18 511 755
spoel at xray.bmc.uu.sespoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Mark Abraham

2006-09-11 13:14:10 UTC

Permalink

Post by Una Bjarnadottir
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system

adding

Post by Una Bjarnadottir
3 Cl ions with genion. When
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

Read closely - "T-Coupling group", not "group". You choose the T-Coupling
groups from among those in the .ndx file (or from the default groups in
its absence, as you're doing here) and specify them in the .mdp file. Thus
you should look there first of all. You need to use a disjoint set of
T-Coupling groups, so this error is consistent with not having done that.
If you were using .ndx file (which you aren't), it might be possible your
.ndx file doesn't correspond to your post-genion structure and something
weird happens. I'd expect GROMACS woud die with a more helpful error in
such a case though.

Mark

Una Bjarnadottir

2006-09-11 13:58:56 UTC

Permalink

Post by Una Bjarnadottir
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system
adding 3 Cl ions with genion. When running grompp after genion with the
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
which is the last water atom (total in system 33003) and groups 15 and 1
are Cl and protein groups if I on the other hand do not neutralize the
system the run goes fine! When looking into the .ndx file atom 33000 is
in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other).
How can I change the group definitions and make sure the groups do not
overlap and to be unique?
It seems to be something wrong with how the genion works for me. I
followed the tutorial and chose the SOL group and water molecules were
replaced by the Cl ions. Than I modifyed the .top file and took 3 sol
molecules and added the 3 ions.
Please help because have not been able to fix the problem with related
letters on the subject on the list.
Best regards, Una Bjarnadottir
What do your tcoupl groups look like?

tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER otherwise error

Post by Una Bjarnadottir
Could it be System SOL?
The number may be confusing, you should subtract one from them when
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T
coupling group.

I made the indes file after running genion using the .gro output file from genion generating it. Also I thought you would have to subtract one and it was groups 14 and 0 instead of 15 and 1. How would I have the ions part of the solvent T coupling group? By modifying the .top file to
[ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL+CL- 9719

and than the tc-grps in the .mdp file accordingly to that. How will I define SOL and CL- together, I tryed
SOL+CL- and SOL-CL- but Fatal error: No such moleculetype SOL+CL- came for both.

Best regards David for your reply, Una
David.

David van der Spoel

2006-09-11 14:00:20 UTC

Permalink

Post by Una Bjarnadottir

Post by Una Bjarnadottir
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system
adding 3 Cl ions with genion. When running grompp after genion with
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
which is the last water atom (total in system 33003) and groups 15
and 1 are Cl and protein groups if I on the other hand do not
neutralize the system the run goes fine! When looking into the .ndx
file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14
(SOL) and 16 (other). How can I change the group definitions and
make sure the groups do not overlap and to be unique?
It seems to be something wrong with how the genion works for me. I
followed the tutorial and chose the SOL group and water molecules
were replaced by the Cl ions. Than I modifyed the .top file and took
3 sol molecules and added the 3 ions.
Please help because have not been able to fix the problem with
related letters on the subject on the list.
Best regards, Una Bjarnadottir
What do your tcoupl groups look like?

tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER otherwise error

Post by Una Bjarnadottir
Could it be System SOL?
The number may be confusing, you should subtract one from them when
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T
coupling group.

I made the indes file after running genion using the .gro output file
from genion generating it. Also I thought you would have to subtract
one and it was groups 14 and 0 instead of 15 and 1. How would I have
the ions part of the solvent T coupling group? By modifying the .top
file to [ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL+CL- 9719
and than the tc-grps in the .mdp file accordingly to that. How will I
define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal
error: No such moleculetype SOL+CL- came for both.
Best regards David for your reply, Una David.

in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and
15 is CL-)

Post by Una Bjarnadottir
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:46 18 471 4205fax: 46 18 511 755
spoel at xray.bmc.uu.sespoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Tsjerk Wassenaar

2006-09-12 10:37:03 UTC

Permalink

Una,

In your case you can also try the T-coupling groups Protein and
Non-Protein, without providing a .ndx file. However, in general give
some thoughts to temperature coupling (groups) when setting up your
system and try to grasp how groups are treated in gromacs.

Hope it helps,

Tsjerk

Post by David van der Spoel

Post by Una Bjarnadottir

Post by Una Bjarnadottir
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system
adding 3 Cl ions with genion. When running grompp after genion with
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
which is the last water atom (total in system 33003) and groups 15
and 1 are Cl and protein groups if I on the other hand do not
neutralize the system the run goes fine! When looking into the .ndx
file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14
(SOL) and 16 (other). How can I change the group definitions and
make sure the groups do not overlap and to be unique?
It seems to be something wrong with how the genion works for me. I
followed the tutorial and chose the SOL group and water molecules
were replaced by the Cl ions. Than I modifyed the .top file and took
3 sol molecules and added the 3 ions.
Please help because have not been able to fix the problem with
related letters on the subject on the list.
Best regards, Una Bjarnadottir
What do your tcoupl groups look like?

tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER otherwise error

Post by Una Bjarnadottir
Could it be System SOL?
The number may be confusing, you should subtract one from them when
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T
coupling group.

I made the indes file after running genion using the .gro output file
from genion generating it. Also I thought you would have to subtract
one and it was groups 14 and 0 instead of 15 and 1. How would I have
the ions part of the solvent T coupling group? By modifying the .top
file to [ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL+CL- 9719
and than the tc-grps in the .mdp file accordingly to that. How will I
define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal
error: No such moleculetype SOL+CL- came for both.
Best regards David for your reply, Una David.

in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and
15 is CL-)

Post by Una Bjarnadottir
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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Una Bjarnadottir2006-09-08 12:21:02 UTC
Una Bjarnadottir2006-09-11 11:00:00 UTC
David van der Spoel2006-09-11 12:22:22 UTC
Mark Abraham2006-09-11 13:14:10 UTC
Una Bjarnadottir2006-09-11 13:58:56 UTC
David van der Spoel2006-09-11 14:00:20 UTC
Tsjerk Wassenaar2006-09-12 10:37:03 UTC
[gmx-users] genion causing atom to be in multiple T-Coupling groups (2024)
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