[gmx-users] Re: tpbconv extension

Mon Dec 13 18:21:36 CET 2010

No, the point is that in Gromacs version 4.0 (and all versions before) steps
were counted in plain int's, which are 32 bit. In version 4.5 they are 64 bit.

But I would suggest to upgrade to 4.5.3 for performance reasons.
If you can run a microsecond, you are probably running in parallel
over many core and 4.5.3 will also improve your performance.

Berk

> Date: Mon, 13 Dec 2010 18:16:28 +0100
> Subject: Re: [gmx-users] Re: tpbconv extension
> From: rmbio861 at gmail.com
> To: gmx-users at gromacs.org
> 
> Hi Berk,
> 
> Thanks for the suggestion, does the tpr file generated by the options
> mention on PC would work on a server with older version of Gromacs
> i.e. 4.0...
> 
> Ram
> 
> On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> > 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
> >> >>>
> >> >>> ========================================
> >> >>> --
> >> >>> gmx-users mailing list    gmx-users at gromacs.org
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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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