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

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Tue Apr 15 2008 - 16:22:18 CDT

Dear Peter and Victor,

Thanks for you replies.

For the output command, I have been using it to write files for simulation
restart in my simulations. But it just outputs the last time frame of an MD
run and the output is in PDB file format. What I want are separate DCD
trajectories for multiple MD runs with the atomic coordinates written at a
certain frequency. They will be used for further analysis and since the
system I am simulating is very large, they are preferred to be in DCD file
format. It would work for me in any case the program can output multiple DCD
files other than creating one single big DCD file in one simulation. I would
be very glad if you tell me I can do it by reading the manual more. :)

Thanks,
Long

On Tue, Apr 15, 2008 at 4:34 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>
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
> > >
> > >
> >

-- 
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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