[gmx-users] Problem control output for checkpoint file

[Vy Phan]

Thank you so much for the suggestion.

Tuong Vy

2015-05-19 23:15 GMT+09:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> EM is implemented separately from MD, and since people rarely write enough
> trajectory-frame coordinates from EM for I/O to be a serious issue, there's
> no good reason to support XTC writing. You can always use trjconv to
> post-process out the groups or steps you want, etc.
>
> Mark
>
> On Tue, May 19, 2015 at 4:13 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/19/15 10:10 AM, Vy Phan wrote:
> > > Dear Justin Lemku,
> > > I am so thankful for your help
> > > Could you please help me more ?
> > > Here is the way I control output file for energy minimization  step ,
> > >   integrator          = cg
> > > nstcgsteep          = 1000
> > > emtol               = 100.0
> > > emstep              = 0.01
> > > nsteps              = 5000
> > > ; Output control
> > > nstxout             = 0
> > > nstvout             = 0
> > > nstfout             = 0
> > > nstenergy           = 50
> > > nstlog              = 50
> > > nstxout-compressed  = 50
> > >
> > > But, the parameter file in the mdout.mdp  file like this
> > >
> > > ; OUTPUT CONTROL OPTIONS
> > > ; Output frequency for coords (x), velocities (v) and forces (f)
> > > nstxout                  = 50
> > > nstvout                  = 0
> > > nstfout                  = 0
> > > ; Output frequency for energies to log file and energy file
> > > nstlog                   = 50
> > > nstcalcenergy            = 100
> > > nstenergy                = 50
> > > ; Output frequency and precision for .xtc file
> > > nstxout-compressed       = 0
> > > compressed-x-precision   = 1000
> > >
> > >
> > > I do not know why this happen ?
> >
> > IIRC you can't write an .xtc during EM, only during actual dynamics.
> > There's
> > probably some magic that grompp does to translate this, but I've never
> > looked
> > into it.
> >
> > -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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