[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

[Abhishek Acharya]

Dear GROMACS users,

I want to insert my molecule of interest in a simulation box at specific
positions, specified by a dat file.

Now, when I run insert-molecules, I find that on "certain occasions" (yes,
it doesn't happen always.), the program also inserts the molecule
at the origin [0 0 0]. It seems that it is appending the input coordinates
of my molecule, provided with -ci,
to the final coordinate file, something which should not happen.

Is this behavior known? Of course, it is trivial to remove the extra
coordinates, but it becomes an effort if a large number of systems need to
be
generated.

Thank you.

Regards,
Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020
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Re: [gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

[Abhishek Acharya]

Sorry, I forgot to mention one important detail.

I am using gromacs version 2016. I tried gromacs 5.1.2 also; it shows the
same behavior.

Regards,

Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Mon, May 29, 2017 at 1:02 PM, Abhishek Acharya 
wrote:

> Dear GROMACS users,
>
> I want to insert my molecule of interest in a simulation box at specific
> positions, specified by a dat file.
>
> Now, when I run insert-molecules, I find that on "certain occasions" (yes,
> it doesn't happen always.), the program also inserts the molecule
> at the origin [0 0 0]. It seems that it is appending the input coordinates
> of my molecule, provided with -ci,
> to the final coordinate file, something which should not happen.
>
> Is this behavior known? Of course, it is trivial to remove the extra
> coordinates, but it becomes an effort if a large number of systems need to
> be
> generated.
>
> Thank you.
>
> Regards,
> Abhishek Acharya
> Research Associate,
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
>
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Re: [gmx-users] Regarding centering the molecule/protein during Simulation

[Peter Kroon]

Hi,


I would not do this. I would run my simulation as normal (no position
restraints), and center my amino acid in post processing (gmx trjconv
-pbc mol -center ...). You may need to make an appropriate index file.
Alternatively you may want to use -fit instead of -center, but that's a
matter of taste.


Peter


On 29-05-17 08:16, Saumyak Mukherjee wrote:
> Hi Dilip,
>
> To fix the amino acid at the centre of the box first you have to use -c
> flag with editconf. Later, during simulation you have to use
> define=-dposres in the mdp file. This will include the position restrain
> defined in the posre.itp file generated during the use of pdb2gmx.
>
> Best,
> Saumyak
>
> On 29 May 2017 at 10:59, Dilip H N  wrote:
>
>> Hello,
>> I have ran a md simulation of a amino-acid with solvent mixture. Now i view
>> the trajectory in vmd and see tht the amino-acid moves sometimes toward the
>> edge of the box,sometimes towards the corners and so on...
>>  Now how can i centre only the amino-acid to the centre of the box and rest
>> (ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
>> vmd i want to fix only the amino-acid to be in centre,whereas the solvent
>> mixtures to move around during the trajectory...
>> How can i do this,...??
>>
>> Thank you...
>>
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D Student
>>
>>
>>
>>    Sent with Mailtrack
>> > referral=cy16f01.di...@nitk.edu.in&idSignature=22>
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>>
>
>


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Re: [gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Thank you Justin. Here is the link to access the topology 
file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0

By the way, I do not know about your advice. Can you please give me the link?
Kind regards,Mohammad

  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Monday, 29 May 2017, 0:21:10
 Subject: Re: [gmx-users] Genion error
   


On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All, when I wanted to add ions to the system, I got this error:
> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section 
> of file 'gr.top'For more information and tips for troubleshooting, please 
> check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> However, there is 'SOL' molecule type in the [ molecules ] section of the 
> topology file. Can you please help me to solve this problem?

Upload your topology to a file-sharing service and provide the URL to access 
it. 
  There's no way to know what's going on (and I recall giving some previous 
advice about line endings - have you checked this?)

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Atom type CB ERROR

[Kashif]

dear sir

I prepared ligand topology and coordinate file using swiss param tool. Then
I simulate my protein with CHARMM FORCE FILED. After giving command

grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

i found this error

Fatal error:
Atomtype CB not found

Kindly help to resolve this error.

regards

kashif
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Re: [gmx-users] Regarding centering the molecule/protein during Simulation

[Peter Kroon]

Keep discussions on the list.

As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center
...`. In your example this would be:

> gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center*

> vmd  mdx.xtc

If you can't figure it out from here, try `gmx trjconv -h` and read.

Peter


On 29-05-17 12:16, Dilip H N wrote:
> Thank you for reply..
>
> I have ran energy minimization,followed by nvt, followed by md run.
> In this md run mdp (md.mdp),
> nw after the simulation ends, i can view the trajectory by giving
> command as :-
>  gmx trjconv -f md.xtc -s md.tpr -pbc mol -o mdx.trr/xtc/gro
>  
> and nw if i view the mdx.trr/xtc/gro in the vmd as :-
>  vmd  mdx.trr/xtc/gro 
>
> will the amino-acid only be at the centre while viewing it throught
> the trajectory and moving solvent molecules around as usual..??
>
> Or can u kindly help me which r the exact commands tht i need to give
> in order tht while viewing the full trajectory in vmd only the
> amino-acid should be in centre , whereas the solvent molecules should
> move around as usual..
>
> -- 
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> 
>


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Re: [gmx-users] Regarding centering the molecule/protein during Simulation

[Peter Kroon]

Keep discussions on the list. I am not your personal help. I will not
respond to future e-mails to my personal address.


Type `gmx trjconv -h` and read.

Also read
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


On 29-05-17 13:43, Dilip H N wrote:
> Thank you...
> nw the amino-acid is placed in the middle, but i have two solvents as
> mixture (solvent A,B).
> But the problem is tht nw the amino-acid remains in the centre but the
> solvent B is moving out of the box
> How can i solve this issue..??
>
> Thank you...
>
> On Mon, May 29, 2017 at 4:10 PM, Peter Kroon  > wrote:
>
> Keep discussions on the list.
>
> As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center
> ...`. In your example this would be:
>
> > gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center*
>
> > vmd  mdx.xtc
>
> If you can't figure it out from here, try `gmx trjconv -h` and read.
>
> Peter
>
>
> On 29-05-17 12:16, Dilip H N wrote:
> > Thank you for reply..
> >
> > I have ran energy minimization,followed by nvt, followed by md run.
> > In this md run mdp (md.mdp),
> > nw after the simulation ends, i can view the trajectory by giving
> > command as :-
> >  gmx trjconv -f md.xtc -s md.tpr -pbc mol -o mdx.trr/xtc/gro
> >
> > and nw if i view the mdx.trr/xtc/gro in the vmd as :-
> >  vmd  mdx.trr/xtc/gro
> >
> > will the amino-acid only be at the centre while viewing it throught
> > the trajectory and moving solvent molecules around as usual..??
> >
> > Or can u kindly help me which r the exact commands tht i need to
> give
> > in order tht while viewing the full trajectory in vmd only the
> > amino-acid should be in centre , whereas the solvent molecules
> should
> > move around as usual..
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >    Sent with Mailtrack
> >
> 
>  
> >
> >
>
>
>
>
>
> -- 
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student


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[gmx-users] Reg: creation of separate chains in .pdb file

[Syed Azeem]

Hey all,

I simulated a protein-peptide docked complex. Post simulation, I
created an index file selecting only the Protein Group
(protein-peptide complex). Then using editconf, I created a .pdb file
for the same.

When I view the prtn.pdb file, only the protein is available but not
the peptide. Still the prtn.pdb file has coordinates for peptide as
well. The pdb file also lacks a chain identifier, which was present in
the initial structure.

How to overcome this?

Thanks in advance

Azeem
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[gmx-users] g_rms using a structure in trajectory as reference

[Francesca Lønstad Bleken]

Hi,

I am trying to understand how to best use a chose frame in the trajectory as 
reference structure for the analysis when using for instance g_rms or g_rmsf.

For instance, if I want to see how the structure changes with respect to the 
structure 20 ns after the beginning of the simulation.

If I understand correctly I can use the .tpr for the md run, but then the input 
structure is used as reference.
gmx_mpi rms -s protein-md.tpr -f trajout_noPBC.xtc -o rmsd.xvg

I have done what I wish to do by dumping the desired snapshot to a .gro with 
trjconv and using this file for the -s input, and it seems to work fine (but 
with 2 warning messages that should not be problematic in my case) .

The warnings are
WARNING: If there are molecules in the input trajectory file
 that are broken across periodic boundaries, they
 cannot be made whole (or treated as whole) without
 you providing a run input file.

WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

Although these warning messages should not be problematic since the trajectory 
has been fixed so that the enzyme is always at the center of the box and masses 
and radii are not of interest in just this case, I wonder if there is a better 
method
for choosing the reference structure from the trajectory while also keeping the 
info from the .tpr file. I realize I could make a new tpr with grompp, but in 
this case I am making a new .tpr and not keeping the info from the last.


I hope I have managed to explain my question.

Best,

Francesca



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[gmx-users] gmx freevolume

[Federico Gallino]

Dear All,

I would like to put your attention on the output of gmx freevolume.
I cannot understand how the "Molecular van der Waals volume" is computed.
I made some crosschecks from the FFV but I never got the value written by gmx.

E.g:

Free volume 35.97 +/- 0.00 %
Total volume 68.07 +/- 0.00 nm^3
Number of molecules 64 total mass 51773.89 Dalton
Average molar mass: 808.97 Dalton
Density rho: 1263.06 +/- 0.00 nm^3
Molecular volume Vm assuming homogeneity: 1.0635 +/- 0. nm^3
Molecular van der Waals volume assuming homogeneity:  0.6810 +/- 0. nm^3
Fractional free volume 0.168 +/- 0.000

If I use the empirical correlation formula:

FFV=1-density*Vw/MW

I got:

FFV=-0.06326   vs   FFv=0.168   (gmx 
freevolume, see above)


Vice versa if I compute Vw I got:

Vw= 0.748086   vs   Vw=0.6810 (gmx freevolume, see above)

In the manual, it is written that the algorithm come from the paper from Bondi, 
that is similar to the ones from Van Krevelen.

I applied the Van Krevelen group contribution approach and I got:

Vw=0.728  in good agreement with the formula above but in disagreement with the 
output from gmx freevolume


Thank you in advance for any clarifications.

Best regards,

Federico


Federico Gallino, Ph.D.
Computational Science & Engineering

mail: federico_gall...@saes-group.com
T: +39 02 93178316
Fax: +39 02 93178460

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Re: [gmx-users] g_rms using a structure in trajectory as reference

[Abhishek Acharya]

Hello,

AFAIK, only coordintes of the reference file is uses for rmsd and rmsf
calculations. So you can do what you have already mentioned.
However, the choice of input structure may be different for rmsd and rmsf
calculations. Both can take any input coordinate (with same number of
atoms), but for rmsd, the general use case would take the starting frame
and calculate the rmsd for full trajectory to see the overall convergence
to equilibrium structure compared to the input structure.

For rmsf, it would make more sense to take a frame from the equilibrated
segment of the trajectory and run the rmsf analysis on the equilibrated
segment alone.

Regards,
Abhishek Acharya


On May 29, 2017 18:26, "Francesca Lønstad Bleken" <
francesca.l.ble...@sintef.no> wrote:

> Hi,
>
> I am trying to understand how to best use a chose frame in the trajectory
> as reference structure for the analysis when using for instance g_rms or
> g_rmsf.
>
> For instance, if I want to see how the structure changes with respect to
> the structure 20 ns after the beginning of the simulation.
>
> If I understand correctly I can use the .tpr for the md run, but then the
> input structure is used as reference.
> gmx_mpi rms -s protein-md.tpr -f trajout_noPBC.xtc -o rmsd.xvg
>
> I have done what I wish to do by dumping the desired snapshot to a .gro
> with trjconv and using this file for the -s input, and it seems to work
> fine (but with 2 warning messages that should not be problematic in my
> case) .
>
> The warnings are
> WARNING: If there are molecules in the input trajectory file
>  that are broken across periodic boundaries, they
>  cannot be made whole (or treated as whole) without
>  you providing a run input file.
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>  based on residue and atom names, since they could not be
>  definitively assigned from the information in your input
>  files. These guessed numbers might deviate from the mass
>  and radius of the atom type. Please check the output
>  files if necessary.
>
> Although these warning messages should not be problematic since the
> trajectory has been fixed so that the enzyme is always at the center of the
> box and masses and radii are not of interest in just this case, I wonder if
> there is a better method
> for choosing the reference structure from the trajectory while also
> keeping the info from the .tpr file. I realize I could make a new tpr with
> grompp, but in this case I am making a new .tpr and not keeping the info
> from the last.
>
>
> I hope I have managed to explain my question.
>
> Best,
>
> Francesca
>
>
>
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[gmx-users] Making a move using command gromacs/vmd

[Poncho Arvayo Zatarain]

Hello gromacs user: i want to make a movie using a gromacs command. I use this: 
gmx trjconv -s file.gro -f file.trr -pbc -o no jump -ndec 7 -o movie.gro. But 
it mrks me the following error: command line -o does not exist. So, i erase -o 
on "-o no jump" and marks me the error: invalid command: no jump. What is the 
command to obtain movie.gro? Thank you.
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Re: [gmx-users] Genion error

[Justin Lemkul]

On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Thank you Justin. Here is the link to access the topology 
file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0

By the way, I do not know about your advice. Can you please give me the link?


It's somewhere in the archive.  Run the topology through dos2unix and always 
make sure to use a plain text editor.  See if that works.


-Justin


Kind regards,Mohammad

   From: Justin Lemkul 
  To: gmx-us...@gromacs.org
  Sent: Monday, 29 May 2017, 0:21:10
  Subject: Re: [gmx-users] Genion error




On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?


Upload your topology to a file-sharing service and provide the URL to access it.
   There's no way to know what's going on (and I recall giving some previous
advice about line endings - have you checked this?)

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Atom type CB ERROR

[Justin Lemkul]

On 5/29/17 5:06 AM, Kashif wrote:

dear sir

I prepared ligand topology and coordinate file using swiss param tool. Then
I simulate my protein with CHARMM FORCE FILED. After giving command

grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

i found this error

Fatal error:
Atomtype CB not found

Kindly help to resolve this error.



CB is not a standard CHARMM atom type so SwissParam must have created a 
definition for it.  #include its parameters from the topology the server gave you.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Reg: creation of separate chains in .pdb file

[Justin Lemkul]

On 5/29/17 8:00 AM, Syed Azeem wrote:

Hey all,

I simulated a protein-peptide docked complex. Post simulation, I
created an index file selecting only the Protein Group
(protein-peptide complex). Then using editconf, I created a .pdb file
for the same.

When I view the prtn.pdb file, only the protein is available but not
the peptide. Still the prtn.pdb file has coordinates for peptide as
well. The pdb file also lacks a chain identifier, which was present in


If you're having trouble viewing the coordinates, that's a problem with the 
viewer itself.  You say that the coordinates are there (as they should be) so 
there's no reason they can't be visualized if rendered properly.



the initial structure.

How to overcome this?



Add suitable chain identifiers back into the coordinate file.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] g_rms using a structure in trajectory as reference

[Justin Lemkul]

On 5/29/17 8:55 AM, Francesca Lønstad Bleken wrote:

Hi,

I am trying to understand how to best use a chose frame in the trajectory as 
reference structure for the analysis when using for instance g_rms or g_rmsf.

For instance, if I want to see how the structure changes with respect to the 
structure 20 ns after the beginning of the simulation.

If I understand correctly I can use the .tpr for the md run, but then the input 
structure is used as reference.
gmx_mpi rms -s protein-md.tpr -f trajout_noPBC.xtc -o rmsd.xvg

I have done what I wish to do by dumping the desired snapshot to a .gro with 
trjconv and using this file for the -s input, and it seems to work fine (but 
with 2 warning messages that should not be problematic in my case) .

The warnings are
WARNING: If there are molecules in the input trajectory file
  that are broken across periodic boundaries, they
  cannot be made whole (or treated as whole) without
  you providing a run input file.

WARNING: Masses and atomic (Van der Waals) radii will be guessed
  based on residue and atom names, since they could not be
  definitively assigned from the information in your input
  files. These guessed numbers might deviate from the mass
  and radius of the atom type. Please check the output
  files if necessary.

Although these warning messages should not be problematic since the trajectory 
has been fixed so that the enzyme is always at the center of the box and masses 
and radii are not of interest in just this case, I wonder if there is a better 
method
for choosing the reference structure from the trajectory while also keeping the 
info from the .tpr file. I realize I could make a new tpr with grompp, but in 
this case I am making a new .tpr and not keeping the info from the last.



The .tpr file is used to determine masses, bonded connectivity, and periodicity 
settings.  A properly re-imaged trajectory shouldn't have anything to do with 
the latter two, but masses are important.  As the warning above states, 
assumptions will be made.  If this is a normal protein, there's probably no 
issue in doing this.  But it's trivial to simply create a new .tpr file from the 
coordinates in your chosen snapshot for the purpose of analysis.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Making a move using command gromacs/vmd

[Justin Lemkul]

On 5/29/17 3:00 PM, Poncho Arvayo Zatarain wrote:



Hello gromacs user: i want to make a movie using a gromacs command. I use this: gmx 
trjconv -s file.gro -f file.trr -pbc -o no jump -ndec 7 -o movie.gro. But it mrks me the 
following error: command line -o does not exist. So, i erase -o on "-o no jump" 
and marks me the error: invalid command: no jump. What is the command to obtain 
movie.gro? Thank you.



You're just scrambling syntax.  Anything separated by whitespace will be 
interpreted as a new argument.  So "-pbc nojump" is valid, but "-pbc -o no jump" 
is incorrect on two levels (sequential options with no arguments, invalid use of 
a command-line argument).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Non-bonded interaction energy

[Мижээ Батсайхан]

Dear gmx users,

I would like to calculate non-bonded interaction energy between two groups.
I performed mdrun -rerun for the groups. How reliable is sum of LJ and
Coulombic energies? Please, is there any suggestion and discussion?


Best regards,

Mijee
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[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

[Abhishek Acharya]

Dear GROMACS users,

I want to insert my molecule of interest in a simulation box at specific
positions, specified by a dat file.

Now, when I run insert-molecules, I find that on "certain occasions" (yes,
it doesn't happen always.), the program also inserts the molecule
at the origin [0 0 0]. It seems that it is appending the input coordinates
of my molecule, provided with -ci,
to the final coordinate file, something which should not happen.

Is this behavior known? Of course, it is trivial to remove the extra
coordinates, but it becomes an effort if a large number of systems need to
be
generated.

Thank you.

Regards,
Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020
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[gmx-users] calculation of energy of individual water molecules in gromacs

[Saumyak Mukherjee]

Dear users,

I need to calculate the energy of individual water molecules in a 1 nm
shell around protein. That is, there will be n number of energy terms in
each time frame if there are n number of water molecules in the said
hydration shell at that time step. Is there a way to do it in GROMACS?

Thanks and regards,
Saumyak

-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] destruction of the structure of a molecule in water after energy minimization

[Saeed Nasiri]

Dear all

I created the topology and itp files for a molecule manually (the
parameters are not exist in the usual force fields) and build a box of a
molecule and 857 water molecules. The structure of the molecule in water
box is OK. Then the energy minimization step was done by the following
files. After the successful termination, the structure of the molecule has
been destroyed and the atoms of the molecule are spread in the box. In the
following the employed files and the structure of the molecule (in gro
format) before and after minimization (without water molecule) are
presented.
 Any help will highly appreciated.

### before minimization ###
1BMCW1   1.222   1.373   1.397
1BMCW2   1.349   1.331   1.419
1BMCR3   1.308   1.498   1.557
1BM   HCW4   1.148   1.339   1.327
1BM   HCW5   1.408   1.254   1.371
1BM   HCR6   1.318   1.570   1.636
1BMNA7   1.196   1.475   1.486
1BMNA8   1.400   1.408   1.521
1BMC19   1.540   1.411   1.566
1BMH1   10   1.571   1.308   1.584
1BMH1   11   1.541   1.464   1.662
1BMC2   12   1.631   1.482   1.466
1BMHC   13   1.588   1.580   1.446
1BMHC   14   1.630   1.426   1.372
1BMCS   15   1.774   1.494   1.518
1BMHC   16   1.814   1.395   1.542
1BMHC   17   1.774   1.551   1.611
1BMCT   18   1.867   1.563   1.418
1BMHC   19   1.831   1.663   1.394
1BMHC   20   1.969   1.572   1.458
1BMHC   21   1.873   1.507   1.324
1BMC1   22   1.082   1.566   1.484
1BMH1   23   1.032   1.567   1.581
1BMH1   24   1.011   1.532   1.409
1BMH1   25   1.121   1.665   1.461
2Cl  Cl   26   2.283   1.962   0.221

 after minimization ###
1BMCW1   1.030   1.807   0.330
1BMCW2   1.253   0.613   1.483
1BMCR3   0.962   1.561   1.355
1BM   HCW4   0.754   0.906   0.667
1BM   HCW5   1.875   0.398   0.729
1BM   HCR6   0.982   2.417   2.358
1BMNA7   0.291   0.861   1.603
1BMNA8   0.845   0.979   2.444
1BMC19   1.834   0.830   2.413
1BMH1   10   1.844   0.003   1.938
1BMH1   11   1.443   1.743   2.290
1BMC2   12   1.917   1.355   1.566
1BMHC   13   1.404   2.327   1.676
1BMHC   14   1.558   1.096   0.699
1BMCS   15   2.661   1.364   2.237
1BMHC   16   2.317   0.518   1.479
1BMHC   17   2.099   2.175   2.002
1BMCT   18   2.036   1.892   0.626
1BMHC   19   2.109   2.565   1.277
1BMHC   20   2.648   1.892   1.400
1BMHC   21   2.494   1.027   0.829
1BMC1   22   0.417   2.454   1.333
1BMH1   23   0.484   1.849   2.126
1BMH1   24   0.182   1.535   0.847
1BMH1   25   1.280   2.539   0.925
2Cl  Cl   26   2.580   2.241   2.823

# minimum.mdp 
; minim.mdp - used as input into grompp to generate em.tpr

integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 10.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 50  ; Maximum number of (minimization) steps to
perform
define = -DFLEXIBLE

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist   = 1; Frequency to update the neighbor
list and long range forces
cutoff-scheme   = Verlet
ns_type= grid; Method to determine neighbor list
(simple, grid)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

## topol.top


#include "oplsaa.ff/forcefield.itp"


#include "ff_BM.itp"
#include "BM.itp"
#include "Cl.itp"

; Include water topology
#include "oplsaa.ff/tip3p.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[system]
BM Cl

[molecules]
BM1
Cl  1
SOL   857
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