[gmx-users] Velocities from checkpoint

[Tsjerk Wassenaar]

Hi,

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.

Cheers,

Tsjerk
On Jun 20, 2014 12:04 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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