Re: "reinitvel" parameter in config file

From: Lewyn Li (lewynli_at_gmail.com)
Date: Thu Oct 12 2006 - 08:12:12 CDT

Hi Dhiraj and Ana,

     In my opinion, it is better to gradually heat your system up in steps
of 1-5 K, rather than steps of 100 K as you indicated. The reason is that
an abrupt increase in temperature can distort the structure of your
biomolecule and lead to instability.

     I usually use the temperature reassignment commands in the NAMD config
file to heat up a system. You can find out more about these commands at:

http://www.ks.uiuc.edu/Research/namd/2.6/ug/node30.html#SECTION00093400000000000000

     Hope this helps.

LEWYN

On 10/12/06, Ana Celia Araujo Vila Verde <avilaverde_at_engr.psu.edu> wrote:
>
> Hi,
>
> This should do what you need. Note that reinitvels is commented out in all
> but the first temperature.
> # Minimization
> minimize 6000
>
> set temperature 50
> reinitvels $temperature
> langevinTemp $temperature
> run 10000 ;# 20 ps
>
> set temperature 100
> #reinitvels $temperature
> langevinTemp $temperature
> run 10000 ;# 20 ps
>
> set temperature 150
> #reinitvels $temperature
> langevinTemp $temperature
> run 10000 ;# 20 ps
>
> set temperature 200
> #reinitvels $temperature
> run 10000 ;# 20 ps
>
>
> _________________________________
> Ana CÚlia Ara˙jo Vila Verde
> Penn State University
> Department of Chemical Engineering
> Fenske Laboratory
> University Park, PA 16802
> USA
>
> <http://www.gfct.fisica.uminho.pt/Members/acvv>
> Phone: +(1) (814) 863-2879
> Fax: +(1) (814) 865-7846
> avilaverde_at_engr.psu.edu
> http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
> http://www.gfct.fisica.uminho.pt/Members/acvv
> _________________________________
>
> -----Original Message-----
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Dhiraj Srivastava
> *Sent:* Wednesday, October 11, 2006 7:34 PM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: "reinitvel" parameter in config file
>
> Hi all
> i want to restart my simulation after minimization. i want to heat
> my system in the step of 100, 200 and then 310. so do i need to leave the
> "reinitvel" parameter as such or should i comment it out? do i need to set
> the "reinitvel" parameter at each step or only in between minimization and
> equilibration at 100 K?
>
> Thank you for your help.
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:40 CST