On 3/4/13 4:11 PM, Miguel Ángel Mompeán García wrote:
The version I was using this morning was 4.6
In that case, it's probably something worth pursuing. Having the new version
fail when an older version works is curious. Can you please provide all of the
following details:
1. Compilers used to build Gromacs
2. Hardware description
3. mdrun command
4. Complete .mdp file
-Justin
2013/3/4, Justin Lemkul <jalem...@vt.edu>:
On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote:
I have tried the same issue (same system with same mdp file and same
initial configuration as starting structure) and is running without
any problems with GROMACS-4.5.5.
Anyone knows what is happening?
You didn't tell us your Gromacs version in the previous post so the best
guess
is "random bug that was somehow fixed before 4.5.5."
-Justin
2013/3/4, Justin Lemkul <jalem...@vt.edu>:
On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote:
Dear gmx users,
I have successfully performed simulations on a charged peptide. I did a
series of mutations and everything had a happy end. Now I have tried
another mutation (just substitution of Asn to Lys) and I am getting the
well-known
"X particles communicated to PME node Y are more than a cell length out
of
the domain decomposition cell of their charge group"
message error during energy minimization, right at the beginning (step
0).
My energy minimization mdp file looks as follows:
integrator = steep ;
emtol = 1000.0 ;
emstep = 0.02 ;
nsteps = 70000 ;
nstlist = 1 ;
ns_type = grid ;
rlist = 1.0 ;
coulombtype = PME ;
rcoulomb = 1.0 ;
rvdw = 1.0 ;
pbc = xyz ;
I have tried without neutralizing with ions, changing the time step,
changing the integrator and the values for rcoulomb,rlist, etc.
Bad idea. Nonbonded cutoffs are an intrinsic part of the force field.
Changing
them will actually increase your likelihood of failure.
I have changed all the parameteres in the mdp file and I get a smaller
value of particles in the message error, but still a crash.
The box size has also no effect on the message error.
I have checked the starting structure and everything is fine. Mutating
that
Asn to a non-charged residue does not yield any problem, but I want to
study the effect in the Asn--> Lys mutation.
Any hint to solve the error?
If EM stops at the first step, there's usually something
catastrophically
wrong
with the starting configuration. If you've decreased the value of
emstep,
there's little else that will account for such behavior.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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