[gmx-users] Velocities from checkpoint
tsjerkw at gmail.com
Sat Jun 21 08:56:11 CEST 2014
You can also avoid using grompp, and use tpbconv -until instead. You can
then use the .cpt file from the previous part with the updated .tpr to get
the next nanosecond, while having a fully continuous trajectory.
On Jun 20, 2014 12:04 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> On 6/19/14, 4:12 PM, Nilesh Dhumal wrote:
>> 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++))
>> grompp -f md.mdp -c structure_1.pdb -p structure_1.top -o
>> 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
>> rm -f *#*
>> rm structure_1.gro
>> rm structure_1.trr
>> 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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