On 3/1/15 2:46 AM, mah maz wrote:
Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production step(around 500k). I have changed the mdp file several times but it doesn't work. What are the possible causes of problem? Thank you! dt = 0.0001 tinit = 0 nsteps = 2000000 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = cut-off
Plain cutoffs introduce serious artifacts. It appears from the tc-grps below that you have just a CNT in vacuo? If this is the case, you should be using infinite cutoffs (rlist=rcoulomb=rvdw=0)
rcoulomb = 0.9 rvdw = 0.9 rvdw_switch = 0.5 vdwtype = switch
These cutoffs seem totally arbitrary to me; they probably aren't conserving energy well and you're getting heating from artifacts.
-Justin
pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 ref_t = 300 tc_grps = CNT gen_temp = 300 pcoupl = no
-- ================================================== 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.
