Thank you so much for the suggestion. Tuong Vy
2015-05-19 23:15 GMT+09:00 Mark Abraham <mark.j.abra...@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 <jalem...@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 > > > > 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. > -- 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.