On 9/12/12 3:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
my mdp file for the md run looks like this:
define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 5000
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 500
nstenergy = 5
energygrps = Protein Non-Protein
nstcalcenergy = 5
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
gen_vel = yes
gen_temp = 200.0
gen_seed = 9999
constraints = all-bonds
tcoupl = V-rescale
tc-grps = Protein System_&_!Protein
tau_t = 0.1 0.1
ref_t = 298 298
pcoupl = no
freezegrps = Protein_&_!TYP
freezedim = Y Y Y
I added a phosphate (TYP) to my protein and now want to do first a
minimization (which I already did), then a short md run (for the case that
I am in a local minima) and after that again a minimization.
Since I only want to minimize the energy of the phosphate I freezed the
rest of the protein (Protein_&_!TYP).
Since on my cluster I am not allowed to run long jobs I had to divide the
minimization run in several runs. The output of the last run was:
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -7.7264606e+05
Maximum force = 1.6227990e+04 on atom 961
Norm of force = 1.2328220e+02
gcq#192: "It's So Fast It's Slow" (F. Black)
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -7.7264606e+05
Maximum force = 1.6227990e+04 on atom 961
Norm of force = 1.2328220e+02
After this minimization run I wanted to do the md run.
My protein is a membrane protein with its surrounding membrane. I already
did a minimization and md run with this protein but without the phosphate.
The only difference to the time when everything worked fine is the
phosphate.
Does this help you somehow to see the failure?
Your minimization is insufficient. You have a maximum force in excess of 16000
on atom 961. Such a large force explains the crash. You should investigate
what this atom is and what is pushing on it so hard.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
