[gmx-users] g_sas with pbc

andrea carotti andcar at chimfarm.unipg.it
Tue Nov 3 12:24:50 CET 2009

Hi all,
I've already simulated 27 organic molecules in a cubic solvent box. Now
I would like to calculate the SAS of this system. I've a tpr and a trr
with only the molecules inside (without water).
I'm using gromacs 4.0.5.
I've added the box dimension infos to the trr using the command:
trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box
7.3973   7.3973   7.3973
In the reference.pdb  I've also the CRYST informations.
I've modified the gmx_sas.c to bypass the check that turn off
automatically the PBC if solvent molecules are not present.
Unfortunately I've seen that the results with and without taking into
account the PBC are identical.
So my questions are:
1) Is it possible to use the g_sas tool to calculate the SAS of this
kind of system?
2) There are some tricks or trasformations or missing informations in my
input(s) that I could fill before running the analysis?
3)Should I use another type of box? Trasform the trajectory with some
pbc keywords (I've also tried -ur compact without luck)...

Thanks in advance and sorry for the long message

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