On 6/19/14, 4:12 PM, Nilesh Dhumal wrote:
Hello, I am running 30ns simulation divided into 30 1ns simulations. I am saving the velocities each 5fs and I can't run a single 30ns simulation with saving velocities each 5 fs. I am running 30 simulations,each is 1ns. I get the velocities and delete the trajectory and go for next simulation. for (( i = 1; i <= 29; i++)) do grompp -f md.mdp -c structure_1.pdb -p structure_1.top -o structure_1.tpr mdrun -s structure_1.tpr -o structure_1.trr -c structure_1.pdb -e structure_1.edr -g structure_1.log rm -f *#* trjconv -f structure_1.trr -s structure_1.tpr -pbc nojump -o structure_1.gro <<EOF 0 EOF ./dipole_rotational_translational_moment_append.out rm -f *#* rm structure_1.gro rm structure_1.trr done Each simulation Gromacs generate the velocities randomly which are independent on previous simulation. Could it possible to get the velocities based on previous simulation.
You need to pass your .cpt file from the previous run to grompp -t. As it stands now, there is no relationship between the different segments of the run, and based on the fact that you're saying you get random velocities, your .mdp file probably has "gen_vel = yes" in 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 601 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.
