[gmx-users] Dividing an MD run

[badamkhatan togoldor]

Hi, I had almost same issue with this. I am extending my simulation by 20 ns. 
gmx convert-tpr -s ../Production_MD/md0.tpr -f ../Production_MD/md0.cpt -e ../Production_MD1/md0.edr -extend 20000 -o md0.tpr gmx mdrun -nt 2 -deffnm md0 -cpi ../Production_MD/md0.cpt 
Then gromacs says (v5.1.1)
NOTE: Reading the state from trajectory is an obsolete feature of gmx convert-tpr.      Continuation should be done by loading a checkpoint file with mdrun -cpi      This guarantees that all state variables are transferred.      gmx convert-tpr is now only useful for increasing nsteps,      but even that can often be avoided by using mdrun -maxh
NOTE: The simulation uses pressure coupling and/or stochastic dynamics.gmx convert-tpr can not provide binary identical continuation.If you want that, supply a checkpoint file to mdrun
However i supplied that .cpt file in mdrun, why is it mentioning the NOTE!   Or is fine? just ignore this Note!   
Is there any other way to extend my simulation? for example like following command 
gmx mdrun -nt 2 -deffnm md0 -cpi md0.cpt -nsteps -2  
Which one is correct? Tnx
Hatnaa

      From: Mark Abraham <mark.j.abraham at gmail.com>
 To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
 Sent: Friday, 4 March 2016, 23:39
 Subject: Re: [gmx-users] Dividing an MD run
   
Hi,

The log file reports what it's doing and hopefully why... But nobody should
be starting new work with 4.5.x or 4.6.x. They are older, slower, have
fewer features, have more bugs, and are out of maintenance...

Mark

On Fri, 4 Mar 2016 17:34 João Henriques <joao.henriques.32353 at gmail.com>
wrote:

> Hmmm, that's odd. I don't see why though. Maybe Justin or any other gromacs
> guru can help you spot the problem.
>
> P.S.: What did the std out from tpbconv say?
>
> /J
>
> On Fri, Mar 4, 2016 at 4:46 PM, Guillem Prats Ejarque <
> Guillem.Prats.Ejarque at uab.cat> wrote:
>
> > Actually, I'm using GROMACS 4.5.5, so, it is ok for me. I generated the
> > new tpr file with 20 ns
> >
> > tpbconv -s md_8ns.tpr -until 20000 -o md_12ns.tpr
> >
> > and I ran it since the last md checkpoint:
> >
> > mdrun -nt 8 -s md_12ns.tpr -cpi md_8ns.cpt -v
> >
> > But, it runs 20 ns from 0, not 12 ns from 8, as it should do. What am I
> > doing wrong?
> >
> >
> > On 3/4/16 8:32 AM, Jo?o Henriques wrote:
> > > tpbconv is the answer for an extension. Choose between -extend or
> -until,
> > > it's up to you. I like -until, because I'm too lazy to do subtractions
> :)
> > >
> > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> > >
> >
> > Correct, though that page is a bit out of date, as tpbconv has been
> renamed
> > convert-tpr.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
> >
> > ------------------------------
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