[gmx-users] Problem control output for checkpoint file

[Justin Lemkul]

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

==================================================