Re: [gmx-users] Scripting Analysis tools in tcsh

[Olli Lehtonen]

On Fri, 30 Jun 2006, Arneh Babakhani wrote:

 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

You are probably having an extra space in front of the latter + sign. Now
+ and end are considered as input for g_hbond.

Olli

PS. For general shell script questions a newsgroup like comp.unix.shell is
a good place to keep in mind.
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[gmx-users] A problem with periodic boundary conditions

[Olli Lehtonen]

Hi all,

While running an energy minimization with mdrun 3.3.1, I observed that
different peptide units in the simulation box were translated in y
direction out of the box, each by N*Ly, N=1,5 (N is peptide unit and Ly is
the box y-dimension). The final structure (confout.gro) is a kind of
staircase instead of beta sheet which I'm trying to simulate.

Only one peptide and all solvent (water and Cl-) remain in the original
box. This happens even after setting nsteps=1. My system is probably quite
far from equilibrium but this kind of behaviour seems anyway unexpected.

I used genconf to generate the initial structure (which looks fine) and it
is these generated units which become translated with mdrun. Any
suggestions how to solve this problem are welcome.

best regards,

Olli
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