[gmx-users] Problem control output for checkpoint file

[Mark Abraham]

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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