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

[Justin A. Lemkul]

Adwait Mevada wrote:
> 
>> 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

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

> 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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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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