From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Tue Mar 14 2006 - 13:18:04 CST
Thanks Leandro,
I guess I will use an external script then. Should be quite convenient.
-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
===================================================
On Tue, 14 Mar 2006, [ISO-8859-1] Leandro Martínez wrote:
> 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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