Re: Defining Temperature for Langevin for Namd restart.

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Aug 05 2009 - 16:36:23 CDT

Hi Amr,

You don't want to comment out the langevinTemp or corresponding
parameter in the barostat. These parameters are different than the
actual temperature of the system. The former merely sets the target
for the thermostat (don't comment out "set temperature"). The later is
determined from your restart .vel file. When you restart a simulation
you comment out the "temperature" parameter (different than the TCL
variable "temperature" you set).

Hope that helps.

Josh

On Aug 5, 2009, at 2:20 PM, Amr Zeinalabideen Majul wrote:

> Thanks for the reply,
>
> the reason I asked was because I got a Fatal error when I commented
> out the langevinTemp. I also took care of thelangevinPistonTemp
> $temperature line.
>
> Your reply leads me to believe that I must have something else wrong
> in the configuration file, probably I did something wrong in
> redefining my Periodic Boundary conditions.
>
> I will look over it and if I can't figure it out I will post the
> config file.
>
> Thanks,
> Amr Majul
>
>
> ----- Original Message -----
> From: Roman Petrenko <rpetrenko_at_gmail.com>
> Date: Wednesday, August 5, 2009 4:13 pm
> Subject: Re: namd-l: Defining Temperature for Langevin for Namd
> restart.
>
>> 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
>>
>>
>

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