On 8/20/15 7:49 AM, anu chandra wrote:
Dear gromcas users, I carried out a continuation of previous md run for nsteps of 5000000 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2
This is redundant. If you restart like this (you should use gmx convert-tpr for simple extensions, as grompp has issues preserving pressure coupling information), then you don't need -cpi when executing mdrun.
The mdp file following run parameters, *************************************************** integrator = md dt = 0.002 nsteps = 5000000 ; nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 20000 compressed-x-grps = System ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 ; pbc = xyz ; gen_vel = no ; tcoupl = Nose-Hoover tc_grps = Protein POPC CL_SOL tau_t = 0.5 0.5 0.5 ref_t = 305.0 305.0 305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC CL_SOL ; refcoord_scaling = com ************************************************************** Though the run completed successfully, I just noticed from the log file that the simulation carried out only for 3500000 steps, instead of 5000000 steps. It looks to me that the simulation started from the previous run that completed 1500000 steps and the current run went from the next 3500000 steps to complete the total run for 5000000 steps. Why this happened? Why it counted total run as 5000000 steps rather than continue the current for another 5000000 steps?
Yes, because of the redundancy above.
Also, I also noticed that the XTC file is written with 176 frames instead of 175 frames (i.e. 3500000/20000)? Is it writing the last step of the previous run again?
The frame at t=0 is always written to the .xtc, so you always have (nsteps/nstxout-compressed)+1 frames.
-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.
