[gmx-users] avoiding bad contact in continutation run

[Mark Abraham]

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.

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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