Re: Defining Temperature for Langevin for Namd restart.

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Aug 05 2009 - 16:35:14 CDT

The Langevin Constant Temperature Control is a thermostat which ensures
that the temperature in the system remains around 310 K. You should not
comment out the "set temperature" line. NAMD will read the restart
velocities and use Langevin thermostat to keep the temperature close to
310 K.

Gianluca

On Wed, 5 Aug 2009, Amr Zeinalabideen Majul wrote:

> 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
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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