Re: How to write different DCD files for separate MD runs in one simulation?

From: V.Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Tue Apr 15 2008 - 15:52:07 CDT

Actually, Peter, you might be right! looks like `output' applies only to
the restart files, not dcd. Ouch, we should all read the manual...
Cheers,
Victor

On Tue, 2008-04-15 at 15:34 -0500, Peter Freddolino wrote:
> Apparently I should read the manual too... thanks for pointing that out
> Victor...
>
> V.Ovchinnikov wrote:
> > You should read the manual, Long.
> >
> > For example
> > http://www.ks.uiuc.edu/Research/namd/2.6/ug/node11.html#SECTION00052200000000000000
> > tells you what the `output' keyword does with multiple runs.
> >
> > Victor
> >
> > On Tue, 2008-04-15 at 14:55 -0400, Yinglong Miao wrote:
> >
> >> Hi,
> >>
> >> I have a question about how to write different DCD files for separate
> >> runs in one NAMD simulation. In one of my simulations, I tried the
> >> following:
> >>
> >> DCDfile ${outputname}_1.dcd
> >> run 200
> >> DCDfile ${outputname}_2.dcd
> >> run 200
> >>
> >> But it turned out that I cannot name different DCD files for the two
> >> run parts like this:
> >>
> >> TCL: Setting parameter DCDfile to 1cwp-vmd-H-out_2.dcd
> >> FATAL ERROR: Setting parameter DCDfile from script failed!
> >>
> >> So I am writing to check whether NAMD 2.6 provides such an option. If
> >> so, what did I do wrong? If not, can anybody tell me how to modify the
> >> source code easily for my purpose? Your help will be greatly
> >> appreciated.
> >>
> >> Thanks,
> >> Long
> >>
> >>
> >> --
> >> Yinglong Miao
> >> Ph.D. Candidate
> >> Center for Cell and Virus Theory
> >> Chemistry Department, Indiana University
> >> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> >> Tel: 1-812-856-0981
> >>

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