[gmx-users] mdrun output structure
Samuel C Flores
samuel.flores at yale.edu
Fri Jun 30 22:23:17 CEST 2006
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?
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:
> 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 <<+
> 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.
I will give you a csh script (of course, between  lie your file names):
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]$c.xvg -b [time]
@ n = ($n + 1)
@ c = ($c + 1)
> Any suggestions?
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