Hi,
Although your preparations seem sensible and a good starting point for stable
simulations, I suspect that the source of the error is in your mdp-file or in
how you constructed your simulation box. I've simulated complexes like yours
for hundreds of nanoseconds without problems. Could you
Hi Erik,
I guess you want to see the production mdp file. Here it is:
; VARIOUS PREPROCESSING OPTIONS
title= Production Simulation
cpp = /lib/cpp
define = -DPOSRES_DNA
; RUN CONTROL PARAMETERS
integrator = md
tinit
The problem could be gen_vel=no if you are not loading velocities that are
consistent with your production temperature of 200 K. If, for example, you do
not load any velocities at all, then the initial forces will quickly be scaled
up to reach 200 K and this can cause large scale
The problem could be gen_vel=no if you are not loading velocities that are
consistent with your production temperature of 200 K. If, for example, you do
not load any velocities at all, then the initial forces will quickly be scaled
up to reach 200 K and this can cause large scale
down
the problem and having a reliable simulation system by the time of your
presentation.
Chris.
-- original message --
Matthias Ernst Matthias.Ernst2 at student.kit.edu
Thu Sep 6 17:55:43 CEST 2012
Previous message: [gmx-users] Effect of refcoord_scaling
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refcoord_scaling is only required when you are also using positions restraints.
Therefore we need to know what exactly you are doing with position restraints
in order to provide the most useful advice.
Nevertheless, you ran 2 simulations and got different results. It is not
prudent to
assign
As a side note: I would be very interested to know what type of artefacts one
might expect when using refcoord_scaling=no with pressure coupling. I have no
doubt that the description in the manual is accurate, but it is also kind of
cryptic to those of us who don't already understand it.
Thank
Hi Chris,
thank you for your answer.
Let me comment on some of your hints.
refcoord_scaling is only required when you are also using positions restraints.
Therefore we need to know what exactly you are doing with position restraints
in order to provide the most useful advice.
Yup, that's right,
Dear Gromacs users,
I am currently working on Protein-DNA-complexes. They should be
simulated in NPT-ensemble.
I did the same simulation including previous minimization steps (in
vacuo, with solvent, with solvent and ions) and equilibration (system
position restrained, with theromstate, with
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