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

[Adwait Mevada]

>>>    1. Re: avoiding bad contact in continutation run (Mark    Abraham)
>>> 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
>> 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 &
>>
>
> Yes, that would be an appropriate set of commands to extend the run.
>
one final query, i need the new tpr to have a different output  
frequency than the older one, is there a way to achieve that.
Thanks,
-Adwait
> -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
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>
> --
> ========================================
>
> 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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> End of gmx-users Digest, Vol 81, Issue 141
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>



-Adwait

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