Hi,
You are right, I had to delete some water molecules, it is working fine now.
Thanks.
-Nisha P
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hi Justin,
I am trying to plot rdf of one methane molecule in water (spc
water, 1095(water molecule in my file). I did create the file using
genbox (31.010 31.010 31.010). This is the energy minimization
file I am using:
Surely a 31-nm cubic box is excessive for a system of 1095 water
molecules. You are aware that Gromacs specifies all units in nm, not
Angstrom, right?
As for the parameters in the .mdp file, I don't see anything that would
necessarily cause the instability you're seeing. A better coulombtype
method (in general) is PME, but this may not have a significant effect
during the EM procedure.
title = Methane in water
cpp = /lib/cpp
include = -I../top
integrator = steep
emtol = 1.0
nsteps = 100
nstenergy = 10
nstxtcout = 10
xtc_grps = CH4 SOL
energygrps = CH4 SOL
nstlist = 5
ns_type = simple
rlist = 1.0
coulombtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
constraints = none
pbc = no
I tried reducing the steps (to 9 instead of 100) and it works but
it doesn't make sense. I am going to try to build the system again.
Reducing the number of steps will actually make the energy minimization
worse! If anything, use *more* steps to try to make the structure
better.
-Justin
Thanks alot of for help.
-Nisha
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hi, I tried energy minimization and I am getting the error while
I am running the minimization step. But then I still tried to
carry on with normal md-simulation, and it was fine, but I am
sure it won't give me the result that it should. Is there a
reason for that? I have tried very low energy steps as well, but
I am still getting the error.
If minimization still reports the same problems, then what I said
before is still true - you have bad contacts somewhere. Have you
looked at the trajectory to see where these problematic atoms are and
what might be causing the clashes?
Sometimes running sufficiently gentle equilibration can relax away some
of these bad contacts, but that is rarely the case and often problems
will manifest later on in the course of MD. I would seriously consider
re-evaluating however you built your system (which you haven't told us)
and try to get the energy minimization to actually work before just
plowing ahead with fingers crossed.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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