Defining Temperature for Langevin for Namd restart.

From: Amr Zeinalabideen Majul (amajul_at_gmu.edu)
Date: Wed Aug 05 2009 - 14:20:15 CDT

Hello all,

Im trying to continue a simulation of a peptide in water, which I have run for 200 picoseconds, and wish to continue the simulation for 200 more seconds.

All the example files out there are very clear about commenting out the initial setting of the velocity temperature, so I have the following:-

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure sp1_wb.psf
coordinates sp1_wb.pdb
bincoordinates sp1_output.restart.coor
binvelocities sp1_output.restart.vel

# set temperature 310
set outputname sp1_400_wb

firsttimestep 100100

So now how do I deal with the langevinTemp variable under Temperature Control?

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

If I comment it out, will ti automatically use the temperature in the .vel file? Or do I have to define the langevinTemp to be the temperature in the .vel file?

Thanks in advance

Amr Majul

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