and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top?
On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury <iitd...@gmail.com>wrote: > On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani > <n.staffol...@unitus.it>wrote: > > > Dear Chandan, > > > > thank you for your reply. Anyway, before making any change to my GROMACS > > and therefore risking to "destroy", can I ask again your advice? > > > Sure. > > > > > From what I have read about environment > > variables<http://en.wikipedia.org/wiki/Environment_variable#Unix>, > > if another simulation is already running on a computer and I want to > > launch > > my simulation but using a different topology, and if my new topology is > > stored in the directory somewhere/my_topology, then I should send the > > following command (for example for a md.com command): > > > > $GMXLIB=somewhere/my_topology md.com > > > > Right? > > > > And is it true that the by doing so, I will affect only this simulation, > > i.e. I will have changed the path to the topology only for this run, > while > > for all the next ones the old path (/usr/share/gromacs/top) will be kept? > > > > > I do not understand where your confusion lies. BTW, Gromacs works in the > following way: > 1. pdb2gmx generates the topolopy file (human readable). > 2. grompp reads this topology and the structure file to generate a tpr > (binary > file). > In the process of generating the tpr file, it reads the force field (FF) > files. The location of the FF is taken from the GMXLIB variable. GMXLIB may > point to any path of the computer where the FF is kept. > 3. You can use this tpr file, to run your simulation to which every > computer you want (gmx should be installed). > If a simulation is already running, then your simulation would take more > time to complete. Your tpr file will not be affected by the previous > simulation. > > The same is also told by Justin. > > Thank you, > > > > Nicola > > > > -- > Chandan Kumar Choudhury > National Chemical Laboratory, Pune > India > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Nicola Staffolani PhD Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics> Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
