[gmx-users] Problem control output for checkpoint file

[Vy Phan]

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 ?
Tuong Vy



2015-05-19 22:39 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 5/19/15 9:24 AM, Vy Phan wrote:
>
>> Dear Gromacs Users!
>> I am a beginner. I am looking for the command line corresponding with
>> nstcheckpoint (control the output of the checkpoint file) in the Gomacs
>> 5.0.4 but I coudn't find. And when I check the log file, I also can not
>> recognize what command line which controls cpt file.
>>
>>
> Read the mdrun help information:
>
>  -cpt   <real>   (15)       Checkpoint interval (minutes)
>
>  The second question, when I run energy minimization I got only one frame,
>> I
>> try to reduce the frequency saving the coordinates but I still get the
>> same
>> result (it look the control output did not working ). I want to save more
>> frame to see what happen in the energy minimization step . Can some one
>> help me?
>>
>>
> If EM finishes in one step, either (1) the structure was already minimized
> or (2) EM failed.  The .log file will tell you happened.
>
>  The third question, I want to generate only the xtc file (I do not want to
>> generate the trr file). What command I need to use for Gromacs 5.0.4 ? (I
>> know the command constxtcout when I search on google, but I can not find
>> the information for it on gromacs manual 5.0.4)
>>
>>
> nstxout-compressed is the current keyword.  Suppress the .trr by setting
> nstxout, nstvout, and nstfout to zero.
>
> Make sure you do some basic tutorial material; these elements are all
> covered by most, if not all, of them.
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>