thank you!
On Wed, May 21, 2014 at 4:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/21/14, 9:06 AM, Nicola Staffolani wrote: > >> just to improve my knowledge in programming: and I can override it by >> typing: >> >> GMXLIB="address_of_the_new_topology_in_my_computer" >> >> right? >> >> > The details depend on your shell. For csh you need setenv, for bash you > need export, etc. Quotes shouldn't be necessary, e.g.: > > export GMXLIB=/home/justin/software/gromacs/custom/share/top > > > But in that case, if I first open a child shell, then the change will be >> effective only there, and as soon as I come back to the parent shell, >> GMXLIB will be pointing to the old /usr/share/... address, right? >> Thank you Justin! >> >> > Any new shell you open will need the environment variable to be set again; > if it's something you need often (or always) set it in .bashrc, .cshrc, etc. > > -Justin > > > PS I do not think I will try to override it anyway ;) And yes, I manually >> installed GROMACS because I didn't know I could do it by just using Ubuntu >> Software Center... >> >> >> On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 5/21/14, 8:38 AM, Nicola Staffolani wrote: >>> >>> and so how do I make GMXLIB point to somewhere else than >>>> /usr/share/gromacs/top? >>>> >>>> >>>> If Gromacs is installed in /usr/share/gromacs, that's where it should >>> point. Otherwise, just override it by setting $GMXLIB in your shell >>> however >>> you like. Hopefully it won't break anything by doing that. >>> >>> -Justin >>> >>> >>> >>> 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. >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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. >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.