Re: MD in a loop with different names for dcd files

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Tue Mar 14 2006 - 12:41:32 CST

Dear Himanshu,
I think someone have asked this before in the list. As I recall, you simply
cannot change the name of the dcd file during the simulations, because the
file is opened only once. I have tried also to move or rename the file, but
in this case the simulation stops. I think the only way of doing that is to
do an script from outside namd to call namd several times, each time
starting the simulation from the previous one and, then, changing the output
name for each independent simulation.
Leandro.

-----------------------------------------
Leandro Martinez
Instiute of Chemistry
State University of Campinas, Brazil
http://www.ime.unicamp.br/~martinez/packmol
-----------------------------------------

On 3/14/06, Himanshu Khandelia <hkhandel_at_dtc.umn.edu> wrote:
>
> Correction to the email:
>
> "However, I still get only one dcd file name system-1.dcd (containing the
> entire trajectory), and I get .vel, .xsc, and .coor file with the prefix
> system-4."
>
>
> ===================================================
> Himanshu Khandelia
>
> Doctoral Candidate,
> Kaznessis Research,
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
>
> Mailing Address:
>
> 499, Walter Library,
> 117, Pleasant St. SE,
> Minneapolis, MN 55455
>
> Phone(o): 612-624-4945
> ===================================================
>
>
> On Tue, 14 Mar 2006, Himanshu Khandelia wrote:
>
> > Hi,
> >
> > I want to run an MD in NAMD, such that I get a new trajectory file every
> > 100 ps, with a new name. For example, the trajectory names would be
> like:
> >
> > system-1.dcd # this trajectory is for 0-100ps
> > system-2.dcd # this trajectory is for 100-200ps
> > system-3.dcd # this trajectory is for 200-300ps
> > ...
> >
> > For this I tried to use the following loop in the config file.
> >
> > ##########################################
> > set start 20
> > set I 1;
> > while { $I < 5 } # stop after 4 runs thru the loop <=> 400 ps
> > {
> > outputname system-${I}
> > firsttimestep $start
> > run 50000 # run for 100ps
> > set I [expr $I + 1]
> > set start [expr $start + 50000]
> > }
> > ##########################################
> >
> >
> > Can someone please tell me where I am wrong? Thank you !
> >
> > -Himanshu
> >
> > ===================================================
> > Himanshu Khandelia
> >
> > Doctoral Candidate,
> > Kaznessis Research,
> > Department of Chemical Engineering and Materials Science,
> > University of Minnesota
> >
> > Mailing Address:
> >
> > 499, Walter Library,
> > 117, Pleasant St. SE,
> > Minneapolis, MN 55455
> >
> > Phone(o): 612-624-4945
> > ===================================================
> >
>

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