[gmx-users] Velocities from checkpoint

Justin Lemkul jalemkul at vt.edu
Fri Jun 20 00:04:16 CEST 2014

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
> ./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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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