On 1/16/13 3:56 AM, Neha Gandhi wrote:
Dear Help,
I am trying to run REMD simulations and found couple of interesting
discussions on GROMACS mailing list regarding ensembles which can be used
during REMD.
I will be running REMD of small peptide in explicit solvent and I am
confused about gen_temp and gen_vel parameters for these simulations below:
1. NPT ensemble at 310 K to get density right. What should be the
parameters gen_vel and gen_temp set to?
That depends. If you do prior equilibration, like NVT, then you should not be
re-generating velocities upon moving to NPT. If NPT is your first phase of
equilibration, then gen_vel = yes and gen_temp is set to whatever the desired
temperature is. The same is true for any equilibration protocol.
2. Equilibration at each temperature -NVT ensemble. Although equilibration
run will be carried out for a reference temperature range, should the
gen_temp still be set to 310K?
If gen_vel = no, then the gen_temp setting is ignored. You should only ever
initialize velocities once, at the start of whatever the first phase of
equilibration is. Regenerating velocities later makes the previous
equilibration pointless and may cause instabilities in your system.
3. Replica exchange -What should be gen_temp and gen_velocity set to?
See point #2.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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