Justin,
I'm using gromacs 4.5.5 version, compiled in double precision. I tried to
generate the .tpr file 3 times and got the same results. About the
gmxcheck, i don't know how to use it to check my .edr file.
How can I do this?
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Marcelo Depólo Polêto
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gmx-users mailing listgmx-users@grom
I have set nstenergy=100. I'm using gromacs compiled with double precision
and even so, the stepsize was too small.
i have faced this convergence problems earlier, and managed some solutions.
I'm really wondering about the warning part, that I have never seen.
--
Marcelo Depólo Polêto
--
gmx-user
Thanks, Elton.
I appreciate your answer, but my question was about the Warning error. The
convergence value was set ok. The minimization do not go further because
the error:
*"WARNING: there may be something wrong with energy file prt_cg.edr
Found: step=-1, nre=36, nblock=0, time=-1.
Trying to sk
Hi Eduardo,
Some visualization softwares completes the structure, even if it's broken.
I suggest you to look at the .pdb file directly in notepad and check out
the composition of your HIS415.
Regards
--
Marcelo Depólo Polêto
Molecular Animal Infectology Laboratory - LIMA
Department of Biochemis
I'm gonna check all this informations, Chaban.
I'm not expert in this field and I have to study much more to follow your
suggestions. Soon, I return with some news.
For now, thanks everyone for your suggestions.
--
Marcelo Depólo
Biochemistry and Molecular Biology Department
University of Viçosa
I thought that at first, but other softwares run in parallel. If there's a
problem, it' s somehow in the PBS.
My guess is that my PBS don't allow the LAM library "see" others nodes. But
I have no clue where the problem could be.
I've tried eliminating the "node=X" and got the error. I've tried use
Hi Erik,
That's good news! But i've got problems using more than one node per
simulation (24 cores per node in my cluster). I don't know if it's a
parallelization
script problem or anything else. I'm using PBS scripts like this:
*#!/bin/bash
#PBS -N Gromacs
#PBS -lselect=1:ncpus=24
#PBS -m ae
#
I recommend use the double precision just to check the better result to
your system. In my case, i've got much better results using emtol=0.004 and
double precision. My system is too much unstable and i tried. I have no
regrets...
Marcelo Depolo
Em 15/09/2012 22:11, "Elie M" es
But if you could simulate the environment just around the ligand, then you
could calculate H-bond and angles energies in a quantum perspective. The
limitation is the lack of integration time, but that can be avoided using a
frame that corresponds to the average system pose.
Or am I too wrong?
--
I am not from the area but I believe that a quantum approach is needed for
proper validation of protein-ligand complex.
Use Gromacs in order to lead you to the best frame (or pose), but calculate
the energies in a quantum perspective.
It probably wasn't a useful comment but i did anyway =)
Good lu
After doing the 'pdb2gmx', created the cell e filled with solvent, use the
"make_ndx" to create an index of your system. One of the groups should be
your residues that you want to freeze. Then, in your .mdp file, use
'freezegrps' and 'freezedim' in your recently created group.
Don't forget the -n
Only the -ignh flag is wrong, as Justin said.
Keep the rest of the command line.
--
Marcelo Depólo
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Dear all,
Is there a consensus on force field choice? I read in this group, people
suggesting compare experimental data and simulation data. But in case of
there's none experimental data about structural data, what to do?
I apologize previously the silly doubt.
Best regards!
--
Marcelo Depólo P
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