Re: Defining Temperature for Langevin for Namd restart.

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Aug 06 2009 - 05:41:17 CDT

sorry, i was wrong then.
in fact, when i had the same problem i just didn't use velocity
restart file (only used coor and xsc restarts), and then you don't
have to make any other changes in md/pressure/temperature control
parameters.

On Wed, Aug 5, 2009 at 5:35 PM, Gianluca
Interlandi<gianluca_at_u.washington.edu> wrote:
> 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.
> -----------------------------------------------------
>
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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