[gmx-users] Fw: problem in extending MD in Gromacs 2018

[Justin Lemkul]

On 11/1/18 7:26 PM, Ladan Mafakhe wrote:
> hi
>
> I saw Gromacs documentary about how to extend MD run but when I used these two commands:
>
> gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr
> gmx mdrun -s next.tpr -cpi state.cpt
>
> my MD run start from the first step. I used these command before without any problem and I wondered what is happen in Gromacs 2018 version.

As Mark said, the .log file will tell you what happened. Copying and 
pasting template commands from the website is not going to lead you to a 
solution because we don't know exactly what you did.

Always provide *exactly* what you did, and relevant output (e.g. from 
the .log file in this case).

-Justin

> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
> Sent: Tuesday, October 30, 2018 6:37:50 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fw: problem in extending MD in Gromacs 2018
>
> Hi,
>
> We can't tell on the information given, because it is how you call mdrun
> that matters, but the 2018 log file will tell you what is wrong. For
> example, if you use gmx mdrun -deffnm md-extended then the output filenames
> all have different names, and it can't know for sure what you intend.
> Various operations are no longer supported in more recent versions, because
> they sometimes led to people losing their files.
>
> See also
> http://manual.gromacs.org/documentation/2018/user-guide/managing-simulations.html#extending-a-tpr-file
>
> More generally, the practice of manually naming all your files with
> numerical suffixes doesn't give you any value. mdrun will do that for you
> with the -noappend option. Or leave the names as default and restarts and
> appending will just work.
>
> Mark
>
> On Tue, Oct 30, 2018 at 3:14 PM Ladan Mafakhe <stud.l_mafakher at pasteur.ac.ir>
> wrote:
>
>>
>>
>> ________________________________
>> From: Ladan Mafakhe
>> Sent: Friday, October 19, 2018 11:17 PM
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: problem in extending MD in Gromacs 2018
>>
>> Hello
>> I use Gromacs 2018 and I have a problem at Extending my MD in this
>> version. I used these commands for extending my MD:
>> gmx convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md-ex.tpr
>> -until 40000
>> or
>> gmx convert-tpr -s md_0_1.tpr -o md-extended.tpr -extend 30000
>> but in both cases, my MD started at beginning steps and not be extended.
>> While I did not have such problem in Gromacs 5. What is my problem and how
>> I can fix it?
>> I really thank you for helping me with this issue.
>> Best regards
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
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