[gmx-users] energy groups for specific parts of the molecule

Dear Gromacs  users, I ran  a simulation between 6 molecules of Hypericin and  26 base pair long DNA, so for energy_grps I set HYP and DNA. Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and  a specific parts of  the DNA(phosphate groups for

Re: [gmx-users] energy groups for specific parts of the molecule

On 7/1/13 7:00 PM, Hovakim Grabski wrote: Dear Gromacs users, I ran a simulation between 6 molecules of Hypericin and 26 base pair long DNA, so for energy_grps I set HYP and DNA. Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and a

Re: [gmx-users] Energy-groups?

:56:04 Subject: [gmx-users] Energy-groups? Hello, I want to plot the interaction potential energy between my solute and solvent. In my .mdp file I did not mention anything under energygrps,so I am thinking it calculates the energies for the whole system. But is there a way I can extract say

[gmx-users] Energy groups

Hi all If I have a topology with set up below (excerpts). And define energy groups in the .mdp file say 'virtsites' and 'endgroup' in correspondence with the index file. Will defining energygrp_exl 'virtsites' and 'endgroup' prevent nonbonding interactions between any atom in either of these

[gmx-users] Energy-groups?

Hello, I want to plot the interaction potential energy between my solute and solvent. In my .mdp file I did not mention anything under energygrps,so I am thinking it calculates the energies for the whole system. But is there a way I can extract say for example LJ-14 term between my

Re: [gmx-users] Energy-groups?

nishap.pa...@utoronto.ca wrote: Hello, I want to plot the interaction potential energy between my solute and solvent. In my .mdp file I did not mention anything under energygrps,so I am thinking it calculates the energies for the whole system. But is there a way I can extract say for

Re: [gmx-users] Energy-groups?

Quoting Justin A. Lemkul jalem...@vt.edu: Thanks Justin! I do want the non-bonded potential between my solute and solvent. So in my .mdp file I put my solute and solvent as energygrps and ran mdrun using this command: mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)

Re: [gmx-users] Energy-groups?

nishap.pa...@utoronto.ca wrote: Quoting Justin A. Lemkul jalem...@vt.edu: Thanks Justin! I do want the non-bonded potential between my solute and solvent. So in my .mdp file I put my solute and solvent as energygrps and ran mdrun using this command: mdrun -s md1.tpr(including energygrps)

Re: [gmx-users] Energy-groups?

I see. It did work . Thanks a lot Justin! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Quoting Justin A. Lemkul jalem...@vt.edu: Thanks Justin! I do want the non-bonded potential between my solute and solvent. So in my .mdp file I put my solute and solvent

Re: [gmx-users] energy groups

Hi, Justin I remove the del command. But I still got an error. make_ndx -f a.pdb -o a.ndx make_ndx.input make_ndx.input: chain A and B !a H* chain C !a H* q checking input for internal consistency... Opening library file /export/apps/share/gromacs/top//ffG53a6.itp Opening library file

Re: [gmx-users] energy groups

Alright, so how about the other comment I made? Are you using the right coordinate file? I recall you got this error when you used the non-pdb2gmx processed .pdb file as input into grompp. You must use the coordinate file that corresponds to your topology. -Justin Liu Shiyong wrote:

Re: [gmx-users] energy groups

pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o r-l_365130_G53a6.minim_traj_withH_0.6.gro r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 21 Hi, Justin grompp read the

Re: [gmx-users] energy groups

Liu Shiyong wrote: pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o r-l_365130_G53a6.minim_traj_withH_0.6.gro r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 21

Re: [gmx-users] energy groups

On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o

Re: [gmx-users] energy groups

Liu Shiyong wrote: Here is my command. pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb Why are you running pdb2gmx twice? Unless you have multiple proteins, and need multiple

Re: [gmx-users] energy groups

command: + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb + editconf -f a6.gro -o a6.gro -d 20.0 + make_ndx -f a.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr b.pdb ATOM 1 N ASP

Re: [gmx-users] energy groups

Alright, none of this looks like it will cause a problem. Can you post your em.mdp file? -Justin Liu Shiyong wrote: command: + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb + editconf -f a6.gro -o a6.gro -d 20.0 + make_ndx

Re: [gmx-users] energy groups

Liu Shiyong wrote: command: + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb + editconf -f a6.gro -o a6.gro -d 20.0 + make_ndx -f a.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr I

Re: [gmx-users] energy groups

Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title = b cpp

Re: [gmx-users] energy groups

Liu Shiyong wrote: Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title

Re: [gmx-users] energy groups

Liu Shiyong wrote: Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title =

[gmx-users] energy groups

Hi, I tried to make energy groups based on chain id and atom type. My purpose is to select atoms in chain A and B without Hydrogen atoms . This is the command: make_ndx -f a.pdb -o a.ndx make_ndx.input a.log cat make_ndx.input del 1-9 chain A and B !a H* chain C !a H* q And then run

Re: [gmx-users] energy groups

Liu Shiyong wrote: --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 150 Fatal error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups

[gmx-users] energy groups

Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely

[gmx-users] energy groups

Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely