[gmx-users] avoiding bad contact in continutation run

Mark Abraham mark.abraham at anu.edu.au
Thu Jan 20 13:32:57 CET 2011

On 01/20/11, Adwait Mevada  <adwait at 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.


> 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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