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 [ma
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 automatically
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 bending,
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
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 i
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. Sin
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