[gmx-users] Question about Extention simulation in REMD

[Qin Qiao]

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..

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.

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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