Re: "reinitvel" parameter in config file

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Thu Oct 12 2006 - 13:03:38 CDT

Hi Lewyn
             thanks for suggestion. its a lot more easy then what i was
doing.
             but i have a problem. initially i am restraining my protein
atoms to move during equilibration and then i want to leave the restrain off
for equilibration. but in this protocol i think the system will goes up to
desired temp say 310.
is it ok to restrain the protein and heat the system up to 310 and then set
the restrain parameter off at 310 or i should do it in some different way.

thanks for your help.

On 10/12/06, Lewyn Li <lewynli_at_gmail.com> wrote:
>
> 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
> >
> >
> >
>

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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