[gmx-users] extending simulation without cpt file

[Hsin-Lin Chiang]

  Hi, Mark

So, You mean I can get correct extending simulation without using -e ede 
and -t trr in GROMACS ver.4.
Then I can set my mind at rest.

Thank you for your reply.

Hsin-Lin
>> Hi, 
>> Today I use serach and find this topic.
>>
>> I got confused.
>>
>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>>
>> According the page of "extending simulation", in GROMACS ver.4, the commend is:
>>
>>
>>
>> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> So you've created a new .tpr with a longer simulation time (but which
> incidentally has the state of the previous .tpr)...
>
>> mdrun -s next.tpr -cpi previous.cpt
> ... and told mdrun to use that longer time, and the current state in the
> checkpoint file. This will work, so long as you are not attempting to
> change the thermodynamic ensemble, or similar.
>
> Mark
>
>> I use this two lines to continue my simulation and get success.
>>
>> But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above.
>>
>> The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before.
>>
>> My GROMACS version is 4.0.5.
>>
>> Am I right to use lines above to do extending simulation?
>>
>>
>>
>> Hsin-Lin
>>
>>
>>
>>> ----- Original Message -----
>>> From: Yongchul Chung<yxc... at case.edu>
>>> Date: Thursday, November 4, 2010 10:28
>>> Subject: [gmx-users] extending simulation without cpt file
>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>>>> Hello gmxers,
>>>> I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
>>>> erased cpt file. However, I need to extend the simulation from the end of
>>>> the trajectory file. I know this will not be binary identical as stated
>>>> here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations).
>>>> I used following commands.
>>>   >
>>>> tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr
>>>> mdrun -s topolnew.tpr
>>>> When I do this and run the simulation, for some reason, the simulation
>>>> starts from t=0 instead of t=102000. it seems like gromacs is writing the
>>>> file without recognizing it that it should start the trajectory from 102000
>>>> ps. Is this a known bug? If so, is there a way around to solve this problem?
>>> You've extended the run time of the original simulation, and forced it to
>>> start from the state in the new .tpr, but that state came from the original
>>> .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the
>>> checkpoint.
>>> Your best chance of continuing will come from reconstructing the .mdp
>>> suitably (use gmxcheck to compare resulting .tpr files) and using grompp to
>>> create a .tpr using the most recent endpoint permitted by your .trr + .edr.
>>
>>
>>   Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I
>>
>>   used it, I'd forgotten :-)
>>
>>
>>
>>   Mark
>>
>>
>>
>>
>>
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