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 <jalem...@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 > > jalem...@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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.