Re: Defining Temperature for Langevin for Namd restart.

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Aug 05 2009 - 17:16:33 CDT

Sorry, why comment out "langevinTemp"? This is needed by the thermostat.
According to the documentation:

langevinTemp < temperature for Langevin calculations (K) >
Acceptable Values: positive decimal
Description: Temperature to which atoms affected by Langevin dynamics will
be adjusted. This temperature will be roughly maintained across the
affected atoms through the addition of friction and random forces.

I agree that "temperature" should be commented out because this is what
assigns the velocities when you start a new simulation. However,
"langevinTemp" has nothing to do with re-assinging the velocities, it is
only used by the thermostat. The velocities will be read in any case, as
long as the parameter "temperature" is not specified.

Gianluca

On Wed, 5 Aug 2009, Roman Petrenko wrote:

> 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
>
>

-----------------------------------------------------
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.
-----------------------------------------------------

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:19 CST