[gmx-users] mdrun output structure

[David Mobley]

Final structure.

On 6/30/06, Samuel C Flores <samuel.flores at yale.edu> wrote:
> Hi Guys,
>
> Quick question:  Is the output structure of mdrun designated by -c a final
> structure, or an average structure?  I want the final structure -- am I
> better off extracting it from the .trr?
>
> Sam
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of paloureiro at biof.ufrj.br
> Sent: Friday, June 30, 2006 1:58 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Scripting Analysis tools in tcsh
>
>
> > Hello GMX users,
> >
> > (this may be more of a tcsh question, but here goes anyway). I'm trying
> > to write a script to go through some trajectories and calculate
> > hbonding.  It looks like this:
> >
> > #!/bin/tcsh
> > foreach number (1 2 3 4 5 6 7 8 9 10 11)
> >        g_hbond -f ../../FullMD/FullMD$number.trr -s
> > ../../FullMD/FullMD$number.tpr -num hbnum-all-$number <<+
> > 1
> > 12
> > +
> > end
> >
> > Here I'm using the g_hbond tool, and I'm trying to automate the process
> > of selecting groups (I want groups 1 and 12). When I run this, the
> > first iteration (number = 1) is executed just fine. Groups 1 and 12 are
> > automatically selected. The analysis is completed, but then the loop is
> > aborted.  (It doesn't go on to number = 2).  There is no error message.
> >
> > Without the "<<+ 1 12 + "  syntax, the loop works just fine (but I have
> > to manually select the groups for each iteration of the loop.  So I
> > think I have a subtle syntax issue here.
>
> Hi,
>
> I will give you a csh script (of course, between [] lie your file names):
>
> #!/bin/csh
>
> set n = 0
> set c = 1
>
>
> while ( $n <= 127 )
>
>
>
>    echo "$n\n" |  g_gyrate_mpi -f [traj].xtc -s [mol].tpr -n
> [index].ndx -o [graph]$c.xvg -b [time]
>    rm '#'*'#'
>     @ n = ($n + 1)
>     @ c = ($c + 1)
> end
>
> > Any suggestions?
> >
>
>
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