Re: Heating in NAMD

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Fri Aug 19 2011 - 12:52:31 CDT

Babban,

You mention that you have consulted the archives and tutorials (which is
good!) but have you also looked at the User Guide, available from the main
NAMD website? The section called "Temperature Control and Equilibration"
describes the details about all these various parameters.

As far as a heating protocol, it probably doesn't make a great deal of
difference how you do it. Personally, for heating my systems I use
something like the second set of commands you mention. Then for production
dynamics, stick with Langevin.

-Erik

On Thu, Aug 18, 2011 at 11:13 AM, Babban Mia <babbanmia_at_gmail.com> wrote:

> Hello
>
> I looked at the archives and tutorials and found two good ways to slowly
> heat up a system in NAMD:
>
> set freq 10
> for {set i 0} {$i <= $temperature} {incr i} {
> langevinTemp $i
> reinitvels $i
> run $freq
> }
>
>
> or
>
> reassignFreq 5
> reassignTemp 0
> reassignIncr 1
> reassignHold 310
>
> Both of the example script already had a langevinTemp set as some value
> (say 310)
> So Do the above scripts reinitialize that value making the LangevinTemp
> redundant ?
> So If I am not further equilibrating my system ,I need not mention/set the
> Langevin Temp 310 before the above heating steps.I was just curious about
> why We need to set the langevinTemp at 310 "under constant temperature
> control" if we are anways going to reinitialize it over the loop and bring
> it some final value at the end of loop.
> Is there a significance to it already ?
>
>
> Which one of the above two methods works the best ?Is there any difference?
> Please advise
>
>
> Best
> Babban
>

-- 
C. Erik Nordgren, Ph.D.
University of Pennsylvania

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