[gmx-users] Re: tpbconv extension

[Berk Hess]

Hi,

I fixed the bug for 4.5.4.

If you want an unlimited number of steps, use:
tpbconv -nsteps -1

Berk

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Re: tpbconv extension
Date: Mon, 13 Dec 2010 17:44:53 +0100








Hi,

No this is actually a bug in tpbconv.
-nsteps will not work, because that uses a normal int, not a 64-bit integer.
-dt should work, but on line 531 of src/kernel/tpbconv.c (int) should be
replaced by (gmx_large_int_t).

But are you sure you want to add a millisecond to your simulation time?

Berk


> Date: Mon, 13 Dec 2010 11:40:50 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: tpbconv extension
> 
> 
> 
> 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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