Re: [gmx-users] Re: wierd behavior of mdrun

Have you tried my suggestion from the last message of setting frequent output? Could your system just be collapsing at the outset of the simulation? Setting nstxout = 1 would catch something like this. There is nothing special about treating a protein in parallel vs. a system of water.

[gmx-users] grompp error in peptide-membrane simulations

Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: Fetal error : Atomtype LC3 not found! (this is atomtype of the lipide) This

Re: [gmx-users] grompp error in peptide-membrane simulations

afsaneh maleki wrote: Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: Fetal error : Atomtype LC3 not found! (this is

Re: [gmx-users] PMF and pull with membrane helix

On Sep 5, 2009, at 7:42 AM, Ragnarok sdf wrote: Hi I am trying to calculate the PMF by pulling two membrane protein monomers apart using the pull code with umbrella sampling. While trying to generate my reaction path, no matter how slow I pull, my helix starts bending (not really

[gmx-users] Re: DMF topology file

Hi Abhishek, I know two possible ways. The first is to find PBD file of DMF (one molecule) and then use x2top program of the gromacs package. When asked for a FF, OPLS/AA can be pointed out. DMF contains only common atoms, so I guess there will be no problems to generate the topology

RE: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun

I have checked my job on another cluster which is dual core. On one node, it just ran fine! I think sth might be wrong with the cluster settings. I will try the output settings you suggested as well. I will keep you posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org