[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)

[Adwait Mevada]

> 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.

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
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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