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

[Ladan Mafakhe]

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.

________________________________
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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