[gmx-users] Question about Extention simulation in REMD

[Qin Qiao]

Thanks! It really is. For the input cpt may have been overwritten before,
when I put it in mdrun again..


2010/12/17 Mark Abraham <mark.abraham at anu.edu.au>

>
>
> On 12/17/10, *Qin Qiao * <qiaoqin47 at gmail.com> wrote:
>
> Thanks!
>
> But still sth strange: I found the total energy is not identical between
> the last frame of the previous REMD and the first frame of the next REMD in
> one replica.
>
> last frame of the previous: 500.000000  -372343.906250
> first frame of the next:          0.000000  -361778.375000
>
> I wonder whether there's some problem and what caused it..
>
>
> OK, we'll need to see the exact sequence of commands that produced your
> observations, i.e. mdrun, then tpbconv, then mdrun. The fact that you're
> managing to get the time reset to zero indicates you've done something
> wrong. As a guess, you didn't use the right .cpt file with the second mdrun
> -cpi.
>
>
>
>
> My setting
> In the .mdp of the previous simulation, gen_vel was on; I didn't record the
> velocity by putting nstvout =0; I used xtcgrp = Protein.
>
>
> These don't matter.
>
> Mark
>
>
>
> Best
>
> Qin
>
> 2010/12/15 Justin A. Lemkul <jalemkul at vt.edu>
>
>>
>>
>>
>> Qin Qiao wrote:
>>
>>> Dear Sir or Madam,
>>>
>>> I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1.
>>> Since I ran a REMD of 56 replicas, there are one cpt file for each replica..
>>> I couldn't do it by
>>>
>>> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
>>>
>>> mdrun -s next.tpr -cpi previous.cpt
>>>
>>>
>>> I guess it's not for an iterative line in the answer in
>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since
>>> the mdrun should run simultaneously.
>>>
>>>
>> The iterative approach Mark describes in that post is for the tpbconv
>> step. Simply extend all of your .tpr files to generate new ones (iterate
>> over all your .tpr files), then proceed with mdrun as you would normally,
>> making use of the -cpi feature.
>>
>> -Justin
>>
>>
>>  Could you give some advice? Thanks.
>>>
>>> Best,
>>>
>>> Qin
>>>
>>>
>> --
>> ========================================
>>
>> 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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