1. Re: avoiding bad contact in continutation run (Mark Abraham)
Adwait Mevada wrote:
On 01/20/11, Adwait Mevada <adw...@imsc.res.in> wrote:
Dear gmx-users,
I am simulating a dppc + chol system, the force field is martini
with gromacs 3.3.3 the system was initially run for 150 ns, but i
had to later extend the simulation, so using the confout.gro and
with mdp options:
gen_vel = no
unconstrained_start = yes
I gave a re-run for another 850 ns, now due to some interaction the
box explodes after 460ns of run.I found that the cause was due to
some unwanted bad contact.
It is important that the system continue from the previous state,
but the extension is leading to this bad contact.
Actually, you didn't preserve your ensemble if you used the .gro file
for the coordinates. See
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Actually
providing us with copies of the commands you're using is always a
good idea when asking for help.
150ns.gro was the output of the previous simulation run i.e. confout.gro
mdp file for the previous simulation is taken as is except for change of
simulation steps and making unconstrained_start = yes
grompp -np 8 -f 850ns.mdp -p dppc_chol.top -c 150ns.gro -o
512lip_256chol_850ns.tpr
As Mark suspected, you have failed to preserve your ensemble, due to the fact
that you're using a reduced precision (.gro) format for coordinates,
and you are
not supplying the .trr and .edr file from the previous run, so you're losing
velocities, temperature and pressure coupling information, etc.
-Justin
so i should be doing something like
tpbconv -s 512lip_150ns.tpr -f 512lip_150ns.trr -e 512lip_150ns.edr -o
512lip_850ns.tpr -extend 850
mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_850ns.tpr
-o 512lip_850ns -e 512lip_850ns -g 512lip_850ns &
mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_256chol_850ns.tpr
-o 512lip_256chol_850ns -e 512lip_256chol_850ns -g 512lip_256chol_850ns &
Mark
My question is, is there a way to avoid this while retaining the
continuation of the previous simulation?
Is using lower precision file a solution to this problem? if yes
how do i go about it.
-Adwait
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-Adwait
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