Re: Defining Temperature for Langevin for Namd restart.

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed Aug 05 2009 - 15:13:57 CDT

just comment out one line
langevinTemp ....

also in namd somewhere comment out something like
temperature ....

temperature value is "hidden" in the atomic velocities, so, yes it is
computed back from velocities on restarts.

On Wed, Aug 5, 2009 at 3:20 PM, Amr Zeinalabideen Majul<amajul_at_gmu.edu> 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
>
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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