[gmx-users] *.ITP file

 Dear Users,  I am trying to generate an *.ITP file for a ligand I am studying using Prodrg server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar hydrogens) while the *.ITP file dispays 37 atoms and it does not display the double bond in the structure, which results in

[gmx-users] dipole moment

Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] *.ITP file

On 5/13/12 5:54 AM, Kowsar Bagherzadeh wrote: Dear Users, I am trying to generate an *.ITP file for a ligand I am studying using Prodrg server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar hydrogens) while the *.ITP file dispays 37 atoms and it does not display the

Re: [gmx-users] dipole moment

On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using

[gmx-users] dipole moment

Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re:

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Again thanks for all your  replies. As I got through your advices, I found that the atoms contribute in making bonds and angles in a residue , or make dihedrals in a residue ( or with atoms in next ones) plus the charge of a the residue should be defined properly in .rtp files to define the new

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/13/12 11:43 AM, Shima Arasteh wrote: Again thanks for all your replies. As I got through your advices, I found that the atoms contribute in making bonds and angles in a residue , or make dihedrals in a residue ( or with atoms in next ones) plus the charge of a the residue should be

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

OK, so I entered the H atom corresponding to the structure and then changed the file as below, [ For ]  [ atoms ] ;  name    type charge   charge group     C   CTL1 0.5700   0     O   O   -0.5700   0     H   HC   0.00 0  [angles ]   ai 

[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

Hello all I am running GROMACS Tutorial: KALP15 in POPC I have compeleted production run 1 ns now I want to extend it for next 1 ns. For this I have used commond: tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt I am getting files are: ener.edr md.log

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Even in gromos87, if I want to make a .rtp file for formyl, I need to put H atom in it? I mean, defining all atoms of a residue is necessary? Aren't the hydrogen atoms set by the gromacs package? Cheers, Shima From: Justin A. Lemkul jalem...@vt.edu To:

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/13/12 12:42 PM, Shima Arasteh wrote: OK, so I entered the H atom corresponding to the structure and then changed the file as below, [ For ] [ atoms ] ; name type charge charge group C CTL1 0.5700 0 O O -0.5700 0 H HC 0.00 0 I find it highly unlikely that a zero charge should be

Re: [gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

On 5/13/12 12:52 PM, Sangita Kachhap wrote: Hello all I am running GROMACS Tutorial: KALP15 in POPC I have compeleted production run 1 ns now I want to extend it for next 1 ns. For this I have used commond: tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/13/12 1:06 PM, Shima Arasteh wrote: Even in gromos87, if I want to make a .rtp file for formyl, I need to put H atom in it? I mean, defining all atoms of a residue is necessary? Aren't the hydrogen atoms set by the gromacs package? No. The presence of hydrogen atoms is set by the

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

  Thanks, It was just a question and I prefer to use the CHARMM36. From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 9:44 PM Subject: Re: [gmx-users] Fatal error: No atoms found in

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

But if the hydrogen has charge and its charge is not zero, then the total charge of formyl wouldn't be zero! Make sense?   Sincerely, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

On 5/13/12 2:17 PM, Shima Arasteh wrote: But if the hydrogen has charge and its charge is not zero, then the total charge of formyl wouldn't be zero! Make sense? This is precisely why I've told you several times that you need to reconsider how you've done your parameterization. If you

[gmx-users] Should I use continuation = yes in my production dynamics following equilibration?

Greetings, I am running 5 ns of equilibration followed by 10 ns of production dynamics. Equilibration and production dynamics differ only in the number of steps and the frequency of saving the positions, velocities, forces, and energies. To conserve disk space, I set nstxout = nstvout = nstfout

Re: [gmx-users] Should I use continuation = yes in my production dynamics following equilibration?

On 5/13/12 9:11 PM, Andrew DeYoung wrote: Greetings, I am running 5 ns of equilibration followed by 10 ns of production dynamics. Equilibration and production dynamics differ only in the number of steps and the frequency of saving the positions, velocities, forces, and energies. To conserve

[gmx-users] Re: Should I use continuation = yes in my production dynamics following equilibration?

Hi Justin, Thanks so much! :-) I checked, and I am using no constraints. However, what if I were? If I did have constraints, then what would you recommend for the continuation keyword? Thanks! Andrew DeYoung Carnegie Mellon University --- If not using constraints, the continuation keyword

Re: [gmx-users] Re: Should I use continuation = yes in my production dynamics following equilibration?

On 5/13/12 9:54 PM, Andrew DeYoung wrote: Hi Justin, Thanks so much! :-) I checked, and I am using no constraints. However, what if I were? If I did have constraints, then what would you recommend for the continuation keyword? Per the description in the manual, it should be set to yes

[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

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[gmx-users] User defined potential

Hi all, I want to define a potential form and give it as input for which i have seen manual ,thought gromacs table option is fine, i have an example of generating 9-6 potential form , My question is how to generate table.xvg, what is the command to generate table.xvg from code table.c.

[gmx-users] mdrun_mpi issue with CHARMM36 FF

Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on