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 _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php