Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi Justin Thank you for your suggestion. I am doing equilibration of DCE (108 molecules) alone in a box and there is no water molecule inside the box. cant i use -DFLEXIBLE for DCE?. by the way i will try your suggestion about xmgrace. In that case, -DF

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi Justin Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big. define = -DFLEXIBLE You should never run MD with flexible water. All the water models included in Gromacs are

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Hi Justin Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big. define = -DFLEXIBLE integrator = md nsteps = 5 dt= 0.002 nstxout

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi justin I found what went wrong and i corrected my mdp file.now the system equilibrated to the desired temperature 300 K (plus r minus 30 K) is this ok? This is impossible to assess without seeing your .mdp settings. A fluctuation of 10% is probably fi

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Hi justin I found what went wrong and i corrected my mdp file.now the system equilibrated to the desired temperature 300 K (plus r minus 30 K) is this ok? Apart from that i want to know how you plot the average running pressure and density in your tutorial for lyzosyme (redline). i just want to d

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi Justin I corrected the mistake what you said and i am able to run energy minimisation and equilibration. but when i view my em.gro and equilibration.gro in VMD it seems to me that the bonds between the atoms are broken in molecules.I used g_energy to che

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Hi Justin I corrected the mistake what you said and i am able to run energy minimisation and equilibration. but when i view my em.gro and equilibration.gro in VMD it seems to me that the bonds between the atoms are broken in molecules.I used g_energy to check weather the system has equilibrated to

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Dear Justin what corrections i should make to ffoplsaan.itp to make it correct. what i should give instead of CAB and CLAA?. You must use atom types, not names. Unfortunately, you've chosen to use atom names, which are also types, which makes all of thi

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Dear Justin what corrections i should make to ffoplsaan.itp to make it correct. what i should give instead of CAB and CLAA?. i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top to my working directory and added these parameters to the corresponding files. what you mean is s

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

On 18/10/10 12:49, vinothkumar mohanakrishnan wrote: Dear Mark I generated the topology using pdb2gmx using dce.pdb. i checked the .top file and i contains necessary .itp files. the error message that i get is given below. any help is highly appreciated. What Mark meant is that you should copy

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi all i added new atomtype for dichloroethane (DCE) and added the corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below are my additions to the corresponding files respectively. *ffoplsaa.rtp* [ DCE ] [ atoms ] CLAA o

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Dear Mark I generated the topology using pdb2gmx using dce.pdb. i checked the .top file and i contains necessary .itp files. the error message that i get is given below. any help is highly appreciated. Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 620 Fatal error: Unknown bond

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

On 18/10/2010 10:31 PM, vinothkumar mohanakrishnan wrote: Hi all i added new atomtype for dichloroethane (DCE) and added the corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below are my additions to the corresponding files respectively. *ffoplsaa.rtp* [ D

[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Hi all i added new atomtype for dichloroethane (DCE) and added the corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below are my additions to the corresponding files respectively. *ffoplsaa.rtp* [ DCE ] [ atoms ] CLAA opls_967 -0.2270 1 CAB opls_966 0.2270