[gmx-users] Re: tpbconv extension

[Berk Hess]

Sorry, I mistook a million ps for a millisecond, this is a microsecond.
The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647.
>From the name of your tpr file it seems you are not exceeding this,
so I don't know what's wrong exactly.

But for this reason (and many other reasons), you might want to consider
upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before).

Berk

> Date: Mon, 13 Dec 2010 17:56:43 +0100
> Subject: Re: [gmx-users] Re: tpbconv extension
> From: rmbio861 at gmail.com
> To: jalemkul at vt.edu; gmx-users at gromacs.org
> CC: 
> 
> Hi Justin and Berk,
> 
> Thanks for the suggestions.
> 
> I am using gromacs 4.0.7 single precision, and would like to extend my
> run each time by 1 microsec as it fits into the wall time on the
> server for my system.
> Please suggest.
> 
> Thanks
> Ram
> On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > ram bio wrote:
> >>
> >> Hi Justin,
> >>
> >> The command was:
> >>
> >> tpbconv -s memb12extnr42000ns.tpr -extend 1000000 -o
> >> memb12extnr43000ns.tpr
> >>
> >
> > Try using -nsteps instead.  There are issues with -extend and -until (bad
> > rounding, limits to the size of the number, etc) that can cause this
> > problem.  I believe all of this has been resolved as of Gromacs 4.5, for
> > future reference.
> >
> > -Justin
> >
> >> Thanks
> >>
> >> Ram
> >>
> >> On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >>>
> >>> ram bio wrote:
> >>>>
> >>>> Dear Gromacs users,
> >>>>
> >>>> I am running a CG simulation for a peptide in lipid bilayer, and the
> >>>> run didnot extend after 42000 ps using gromacs 4.0.7,
> >>>>
> >>>> Reading toplogy and shit from memb12extnr42000ns.tpr
> >>>> Extending remaining runtime of by 1e+06 ps (now -2144967266 steps)
> >>>> You've simulated long enough. Not writing tpr file
> >>>>
> >>>>  Please give your suggestions to overcome this error.
> >>>>
> >>> What was your command?
> >>>
> >>> -Justin
> >>>
> >>>> Ram
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Mon, Dec 13, 2010 at 5:26 PM, ram bio <rmbio861 at gmail.com> wrote:
> >>>>>
> >>>>> Dear Gromacs users,
> >>>>>
> >>>>> I
> >>>>>
> >>> --
> >>> ========================================
> >>>
> >>> 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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> >>>
> >>
> >
> > --
> > ========================================
> >
> > 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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