[gmx-users] g_sas with pbc

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 3 12:43:22 CET 2009

andrea carotti wrote:
> 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
> Andrea
There is an open bugzilla on this


In principle it should work, but there may still be a small bug. Feel 
free to upload a test system to this bugzilla.

> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list