[gmx-users] gromacs 5.0 compile with QM/MM
Dear gromacs users, I am compiling Gromacs 5.0, but can't find how to enable compiling with QMMM funtion like ORCA. would you please tell me how to get it ? Jun Gao Shandong University -- 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.
Re: [gmx-users] gromacs 5.0 compile with QM/MM
Hi. I am not a expert but looking the CMakeLists.txt Did you try the argument cmake ... *-DGMX_QMMM_PROGRAM=orca* ../gromacs Maybe that works Good luck On Wed, Sep 3, 2014 at 2:40 AM, 高军 gao...@sdu.edu.cn wrote: Dear gromacs users, I am compiling Gromacs 5.0, but can't find how to enable compiling with QMMM funtion like ORCA. would you please tell me how to get it ? Jun Gao Shandong University -- 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. -- 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.
[gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi all, I am trying to use trjconv -box -1 -1 14 to modify the z dimention of the box containing DMPC lipid bilayer and water. I have used: trjconv -f dmpc.xtc -pbc mol -center -o dmpc_mol_cent.xtc -s dmpc.tpr trjconv -f dmpc_mol_cent.xtc -o dmpc_newbox.xtc -box -1 -1 14 Both the modified version of trjconv (as reported in http://redmine.gromacs.org/issues/871) and the gmx trjconv of GROMACS 5.0 don't work. The -1 option in -box, for the x and y dimension, don't preserve the original box size but changes these as 0: I obtain a box with dimension 0 0 14. Thanks in advance Stefano -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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.
[gmx-users] Why compute capability or = 2.0??
Dear users, I wish to know why Gromacs has chosen compute capability _ 2.0? why 2 not 1.0? -- 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.
Re: [gmx-users] Why compute capability or = 2.0??
Hi, Because 2.0 has things that are useful, and maintaining two versions of any code is expensive. Mark On Wed, Sep 3, 2014 at 12:46 PM, B P 4grom...@gmail.com wrote: Dear users, I wish to know why Gromacs has chosen compute capability _ 2.0? why 2 not 1.0? -- 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. -- 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.
[gmx-users] All atom MD Simulation
Can we analyse catalytic mechanism of an enzyme using the classical all atom MD simulation. -- 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.
Re: [gmx-users] How to mearg Ligand protein and Lipid
On 9/3/14, 12:46 AM, RINU KHATTRI wrote: hello justin i made tc_group for protein ligand and popc but i have merged protein_ligand_popc and sol_cl i made only two group now im running long simulation what can i do is this two tc_group can create the wrong analysis. No idea. I doubt it will lead to any severe artifacts. Technically speaking, anything other than one thermostat is incorrect but commonplace because of algorithmic problems in many thermostats. -Justin -- == 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.
Re: [gmx-users] All atom MD Simulation
On 9/3/14, 7:40 AM, Anitha wrote: Can we analyse catalytic mechanism of an enzyme using the classical all atom MD simulation. No. -Justin -- == 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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? Thanks, Mark On Wed, Sep 3, 2014 at 11:38 AM, Stefano Borocci boro...@unitus.it wrote: Hi all, I am trying to use trjconv -box -1 -1 14 to modify the z dimention of the box containing DMPC lipid bilayer and water. I have used: trjconv -f dmpc.xtc -pbc mol -center -o dmpc_mol_cent.xtc -s dmpc.tpr trjconv -f dmpc_mol_cent.xtc -o dmpc_newbox.xtc -box -1 -1 14 Both the modified version of trjconv (as reported in http://redmine.gromacs.org/issues/871) and the gmx trjconv of GROMACS 5.0 don't work. The -1 option in -box, for the x and y dimension, don't preserve the original box size but changes these as 0: I obtain a box with dimension 0 0 14. Thanks in advance Stefano -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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. -- 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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
On 9/3/14, 7:52 AM, Mark Abraham wrote: Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? I think this comes from the fact that the code uses clear_mat(fr.box) and then only ever reassigns fr.box[m][m] in the case of newbox[m] 0. If it's -1, then the code does nothing to it, so it stays at zero. Should be a simple fix. -Justin -- == 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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi Justin, I agree with you. The selection -box in trjconv create a new box and change all the dimension; If the value is -1, the original value of dimension (from the xtc file) is not maintained but changed to zero. Thanks Stefano 2014-09-03 14:07 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 9/3/14, 7:52 AM, Mark Abraham wrote: Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? I think this comes from the fact that the code uses clear_mat(fr.box) and then only ever reassigns fr.box[m][m] in the case of newbox[m] 0. If it's -1, then the code does nothing to it, so it stays at zero. Should be a simple fix. -Justin -- == 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. -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Right - fix looks good. No need to do anything, Stefano, unless you'd like to grab the source code and try out the solution at https://gerrit.gromacs.org/#/c/3988/ Mark On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/3/14, 7:52 AM, Mark Abraham wrote: Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? I think this comes from the fact that the code uses clear_mat(fr.box) and then only ever reassigns fr.box[m][m] in the case of newbox[m] 0. If it's -1, then the code does nothing to it, so it stays at zero. Should be a simple fix. -Justin -- == 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. -- 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.
Re: [gmx-users] Why compute capability or = 2.0??
...and because earlier cards were not up to the task of accelerating GROMACS - unless paired with low-end CPUs. -- Szilárd On Wed, Sep 3, 2014 at 1:34 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Because 2.0 has things that are useful, and maintaining two versions of any code is expensive. Mark On Wed, Sep 3, 2014 at 12:46 PM, B P 4grom...@gmail.com wrote: Dear users, I wish to know why Gromacs has chosen compute capability _ 2.0? why 2 not 1.0? -- 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. -- 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. -- 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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi Mark many thanks for your quick solution. I add the new lines to the source code and I try again the change of box size. Thanks Stefano 2014-09-03 14:31 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: Right - fix looks good. No need to do anything, Stefano, unless you'd like to grab the source code and try out the solution at https://gerrit.gromacs.org/#/c/3988/ Mark On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/3/14, 7:52 AM, Mark Abraham wrote: Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? I think this comes from the fact that the code uses clear_mat(fr.box) and then only ever reassigns fr.box[m][m] in the case of newbox[m] 0. If it's -1, then the code does nothing to it, so it stays at zero. Should be a simple fix. -Justin -- == 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. -- 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. -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi Mark it works. trjconv -box -1 -1 14 now change only the z dimension and maintains the original xy value present in the xtc file. Thanks again Stefano 2014-09-03 14:31 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: Right - fix looks good. No need to do anything, Stefano, unless you'd like to grab the source code and try out the solution at https://gerrit.gromacs.org/#/c/3988/ Mark On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/3/14, 7:52 AM, Mark Abraham wrote: Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? I think this comes from the fact that the code uses clear_mat(fr.box) and then only ever reassigns fr.box[m][m] in the case of newbox[m] 0. If it's -1, then the code does nothing to it, so it stays at zero. Should be a simple fix. -Justin -- == 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. -- 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. -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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.
[gmx-users] Making trajectory movie last longer.
Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- 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.
Re: [gmx-users] Making trajectory movie last longer.
Hi, when you say too quickly are you referring to the noise I guess. If it is the case, you could try to filter you xtc either with g_filter in order to reduce the fluctuactions or in vmd itself you can smooth the xtc in the graphical representations - trajectory tab - trajectory smooting (2 or 3 should be enough) hope it helps and On 03/09/2014 15:35, Dawid das wrote: Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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.
Re: [gmx-users] Making trajectory movie last longer.
No, I don't mean noise :). What I mean is that next frame appears on the screen before I can take a good look at previous one. So imagine that you make a presentation and you change each slide after 0.1 s. You can't have a good look at it so let's say I need 2 s to have a good look. I hope now you understand better what I mean. 2014-09-03 14:41 GMT+01:00 andrea andrea.spital...@iit.it: Hi, when you say too quickly are you referring to the noise I guess. If it is the case, you could try to filter you xtc either with g_filter in order to reduce the fluctuactions or in vmd itself you can smooth the xtc in the graphical representations - trajectory tab - trajectory smooting (2 or 3 should be enough) hope it helps and On 03/09/2014 15:35, Dawid das wrote: Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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. -- 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.
[gmx-users] Constraint and Temperature Drop in NVE
Hi. After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run NVE (0.5fs timesteps) with a harmonic restraint with force constant 4184kJ/mol rad^2, the temperature then fluctuate around 292 K ( http://oi60.tinypic.com/sni5at.jpg). When I instead run NVE with same setting except without the constraint after the two equilibration steps, the temperature stays around 300K. What is the cause of this drop of temperature to 292K? Thanks again. -- 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.
Re: [gmx-users] Constraint and Temperature Drop in NVE
Hi. After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run NVE (0.5fs timesteps) with a harmonic restraint with force constant 4184kJ/mol rad^2, the temperature then fluctuate around 292 K ( http://oi60.tinypic.com/sni5at.jpg) in gromacs 4.6.6. When I instead run NVE with same setting except without the constraint after the two equilibration steps, the temperature stays around 300K. What is the cause of this drop of temperature to 292K? Thanks again. -- 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.
Re: [gmx-users] Making trajectory movie last longer.
and then, use a video capture tool to capture the video played at 1/4 speed? On Wed, Sep 3, 2014 at 10:27 AM, Johnny Lu johnny.lu...@gmail.com wrote: is it possible to play the movie slower? Like at 1/4 speed? I don't know if vlc or windows media player supports that. On Wed, Sep 3, 2014 at 9:45 AM, Dawid das add...@googlemail.com wrote: No, I don't mean noise :). What I mean is that next frame appears on the screen before I can take a good look at previous one. So imagine that you make a presentation and you change each slide after 0.1 s. You can't have a good look at it so let's say I need 2 s to have a good look. I hope now you understand better what I mean. 2014-09-03 14:41 GMT+01:00 andrea andrea.spital...@iit.it: Hi, when you say too quickly are you referring to the noise I guess. If it is the case, you could try to filter you xtc either with g_filter in order to reduce the fluctuactions or in vmd itself you can smooth the xtc in the graphical representations - trajectory tab - trajectory smooting (2 or 3 should be enough) hope it helps and On 03/09/2014 15:35, Dawid das wrote: Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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. -- 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. -- 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.
Re: [gmx-users] Making trajectory movie last longer.
I see now. sorry. you want make a movie. yes in vmd have look to change viewer render under visualization. and On 03/09/2014 15:45, Dawid das wrote: No, I don't mean noise :). What I mean is that next frame appears on the screen before I can take a good look at previous one. So imagine that you make a presentation and you change each slide after 0.1 s. You can't have a good look at it so let's say I need 2 s to have a good look. I hope now you understand better what I mean. 2014-09-03 14:41 GMT+01:00 andrea andrea.spital...@iit.it: Hi, when you say too quickly are you referring to the noise I guess. If it is the case, you could try to filter you xtc either with g_filter in order to reduce the fluctuactions or in vmd itself you can smooth the xtc in the graphical representations - trajectory tab - trajectory smooting (2 or 3 should be enough) hope it helps and On 03/09/2014 15:35, Dawid das wrote: Dear Gromacs experts, I have a question not regarding Gromacs itself but maybe you found a solution. I have already solved this problem but not for GROMACS files. I want to make a trajectory movie using VMD, but following frames appear too quickly and it is very hard to actually see and analyze how chromophore structure changes over time. So I want to make the movie last longer and the frames to be be displayed for a longer timer. I did it for Tinker trajectory snapshots by uploading the same snapshot 5 or 7 times but how to do it with *gro and *trr files from Gromacs? Best wishes, Dawid Grabarek PS Maybe you suggest to use different prorgram? -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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. -- --- Andrea Spitaleri PhD Principal Investigator AIRC D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- 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.
Re: [gmx-users] All atom MD Simulation
Can we analyse catalytic mechanism of an enzyme using the classical all atom MD simulation. No. I would say, that is a bit too pessimistic and unnecessarily demotivating. You can not directly simulate the catalytic reaction without employing a quantum chemical treatment (or a reactive force field) for the catalytic site and the reacting compounds, but even without that, just with classical MD, you can still learn a lot about the enzymatic mechanism, e.g., about the binding of a substrate, the stabilization of reaction intermediates with respect to educt(s) and product(s) in the catalytic site relative to the same reaction in solution, the release of a product(s) etc. A literature research will turn up innumerable examples. -- R. Thomas Ullmann, PhD Theoretical Computational Biophysics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen, Germany thomas.ullm...@mpibpc.mpg.de www.bisb.uni-bayreuth.de/People/ullmannt -- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, September 03, 2014 1:42 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] All atom MD Simulation On 9/3/14, 7:40 AM, Anitha wrote: Can we analyse catalytic mechanism of an enzyme using the classical all atom MD simulation. No. -Justin -- == 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. -- 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.
[gmx-users] changing the viscosity of water in a simulation
Date: Tue, 2 Sep 2014 20:02:01 +0200 From: Dr. Vitaly Chaban vvcha...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] changing the viscosity of water in a simulation Message-ID: CAPXdD+ZBQiUfCZrKQgFenNG7_7iQv0SfoO9GeS=m_afv28j...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Tue, Sep 2, 2014 at 10:59 AM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hello, I am a newbie to MD simulation. We are working in the direction of finding the molecular origin of internal friction of protein folding. For this we have to run folding simulations at different solvent viscosity and plot protein reconfiguration time against solvent viscosity. Currently, we have been using TIP3P water molecules for simulations run on GROMACS 4.5.6. I wwill be highly grateful if someone tells me how to change the viscosity of water. To change water viscosity, you must be assigned as God. That is not 100% correct, there are thermostats, which allow to change the transport properties (incl. the viscosity): http://dx.doi.org/10.1016/j.cpc.2008.01.018 Unfortunately the DPD thermostat isn't implemented in Gromacs, so you will have to use another MD package like OpenMM, ESPResSo++ or ESPResSo. Cheers, Christoph Pick up another FFM. Dr. Vitaly V. Chaban ??? ?? ? Best, Soumadwip. -- 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. -- Christoph Junghans Web: http://www.compphys.de -- 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.
Re: [gmx-users] GROM (.mdp, .itp, .top) and .pdb Editor with Syntax Highlighting
It is Great idea but I have some errors with binary ./GROM bash: ./GROM: cannot execute binary file: Ошибка формата выполняемого файла - II don't know how it should look in english but google translate said, that bash: ./GROM: cannot execute binary file: Format error executable with source GROM-master$ python3 GROM.py Traceback (most recent call last): File GROM.py, line 56, in module import grom File /home/user/Загрузки/GROM-master/grom/__init__.py, line 73, in module import PyQt5.QtWebKit ImportError: No module named 'PyQt5.QtWebKit' The packages build-essential python3 qt5-default qttools5-dev-tools python3-pyqt5 were installed before start In the weekend I will run it more carefully I use ubuntu 14.04 32bit -- С уважением, Александр Селютин -- 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.
[gmx-users] Configuration bug preventing GROMACS 5.0 build with Intel compiler?
Hi All, I'm attempting to compile GROMACS 5.0 (as downloaded from the tarball available here: http://www.gromacs.org/Downloads) with Intel Compiler version 14 and Intel MPI version 5 without success. I'm also compiling the CUDA functionality (with CUDA 6.5) but CUDA/MPI functionality doesn't seem to be related to the compilation problem I'm seeing. I'm using CMAKE 3.0.1 which I compiled myself from source with the same Intel 14 compiler. Here is the version info: icc --version icc (ICC) 14.0.3 20140422 Copyright (C) 1985-2014 Intel Corporation. All rights reserved. icpc --version icpc (ICC) 14.0.3 20140422 Copyright (C) 1985-2014 Intel Corporation. All rights reserved. mpirun --version Intel(R) MPI Library for Linux* OS, Version 5.0 Build 20140605 Copyright (C) 2003-2014, Intel Corporation. All rights reserved. I'm compiling like so: module load compiler/intel/14.0/3.174 module load mpi/intel/5.0/0.028 tar -zxvf gromacs-5.0.tar.gz cd gromacs-5.0 mkdir build cd build ../../../CMAKE/cmake-3.0.1_intel14.0/bin/cmake .. \ -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc \ -DGMX_MPI=on -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/app/libraries/cuda/6.5/sb \ -DCUDA_HOST_COMPILER=/app/compilers/intel/14.0.3.174/composer_xe_2013_sp1.3.174/bin/intel64/icpc \ -DCUDA_VERBOSE_BUILD=ON -DCUDA_VER=6.5 -DCUDA_INSTALL_PATH=/app/libraries/cuda/6.5/sb \ -DCMAKE_INSTALL_PREFIX=../../../G2/install \ -DGMX_FFT_LIBRARY=mkl \ -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_VERBOSE_MAKEFILE=ON make make install During install I see the following: file INSTALL cannot find /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/bin/gmx_mpi. Going backwards through the compilation I first see multiple instances of undefined references to _finite and _aligned_free like this one during link: /app/libraries/impi/5.0.0.028/intel64/bin/mpiicpc-mavx -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd1782 -ip -funroll-all-loops -alias-const -ansi-alias -O3 -DNDEBUG -mkl=sequentialCMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs_mpi.so.0.0.0 -openmp ../../lib/libgpu_utils.a ../../lib/libnbnxn_cuda.a ../../lib/libcuda_tools.a /app/libraries/cuda/6.5/sb/lib64/libcudart.so -ldl -lrt -lm -lz -Wl,-rpath,/home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/lib:/app/libraries/cuda/6.5/sb/lib64 ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `_finite' ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `_aligned_free' ...and earlier during compilation: /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/src/gromacs/math/utilities.c(731): warning #266: function _finite declared implicitly returnval = _finite(x); /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/src/gromacs/utility/smalloc.c(359): warning #266: function _aligned_free declared implicitly _aligned_free(free); This seems to be related to the CMAKE configuration successfully finding functions that don't exist on my platform, in particular from: -- Checking for isfinite -- Performing Test isfinite_compile_ok -- Performing Test isfinite_compile_ok - Success -- Checking for isfinite - yes -- Checking for _isfinite -- Performing Test _isfinite_compile_ok -- Performing Test _isfinite_compile_ok - Success -- Checking for _isfinite - yes -- Checking for _finite -- Performing Test _finite_compile_ok -- Performing Test _finite_compile_ok - Success -- Checking for _finite - yes -- Looking for _aligned_malloc -- Looking for _aligned_malloc - found According to build/CMakeFiles/CMakeOutput.log and CMakeError.log all the above checks pass, yet in CMakeOutput.log all except the first check (isfinite) are logged as having undefined references, yet the check still reports success. This is the just the output for _finite_compile_ok but the _isfinite_compile_ok and _aligned_malloc follow a similar pattern: Performing C SOURCE FILE Test _finite_compile_ok succeded with the following output: Change Dir: /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/gmake cmTryCompileExec3947929838/fast /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3947929838.dir/build.make CMakeFiles/cmTryCompileExec3947929838.dir/build gmake[1]: Entering directory `/home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/CMakeFiles/CMakeTmp' /home/paul.caheny/ISV/FY14Q2/GROMACS/CMAKE/cmake-2.8.12.2_intel14.0/bin/cmake -E cmake_progress_report /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec3947929838.dir/src.c.o /app/libraries/impi/5.0.0.028/intel64/bin/mpiicc -std=gnu99 -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415
[gmx-users] GROM (.mdp, .itp, .top) and .pdb Editor with Syntax Highlighting
Hi Alexander, Since you're using Ubuntu 14.04 32 bit, that would explain why there's an error. I freezed the scripts under 64 bit system. And for the source, I've updated source code's readme file, run: sudo apt-get install libqt5webkit5 sudo apt-get install python3-pyqt5.qtwebkit Best regards, Hovakim среда, 3 сентября 2014 20:55 Александр Селютин saga1...@gmail.com писал(а): It is Great idea but I have some errors with binary ./GROM bash: ./GROM: cannot execute binary file: Ошибка формата выполняемого файла - II don't know how it should look in english but google translate said, that bash: ./GROM: cannot execute binary file: Format error executable with source GROM-master$ python3 GROM.py Traceback (most recent call last): File GROM.py, line 56, in module import grom File /home/user/Загрузки/GROM-master/grom/__init__.py, line 73, in module import PyQt5.QtWebKit ImportError: No module named 'PyQt5.QtWebKit' The packages build-essential python3 qt5-default qttools5-dev-tools python3-pyqt5 were installed before start In the weekend I will run it more carefully I use ubuntu 14.04 32bit -- С уважением, Александр Селютин -- 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.
Re: [gmx-users] GROM (.mdp, .itp, .top) and .pdb Editor with Syntax Highlighting
Hi. What is the output of file GROM ? Is it because that GROM file is compiled for 32-bit, instead of 64-bit? On Wed, Sep 3, 2014 at 12:55 PM, Александр Селютин saga1...@gmail.com wrote: It is Great idea but I have some errors with binary ./GROM bash: ./GROM: cannot execute binary file: Ошибка формата выполняемого файла - II don't know how it should look in english but google translate said, that bash: ./GROM: cannot execute binary file: Format error executable with source GROM-master$ python3 GROM.py Traceback (most recent call last): File GROM.py, line 56, in module import grom File /home/user/Загрузки/GROM-master/grom/__init__.py, line 73, in module import PyQt5.QtWebKit ImportError: No module named 'PyQt5.QtWebKit' The packages build-essential python3 qt5-default qttools5-dev-tools python3-pyqt5 were installed before start In the weekend I will run it more carefully I use ubuntu 14.04 32bit -- С уважением, Александр Селютин -- 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. -- 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.
[gmx-users] Moving part # of -noappend
Hi. When gromacs is working on abc.part0010.trr, is it ok to move every file called abc.partDEFG.xyz where DEFG is less than 0010 to another place? And, after that, will gromacs make a new file called abc.part0011.trr instead of another abc.part0001.trr ? (will the part # reset to 0001 if I move some files away?) I want to keep track of the order of the parts, after I move them away. Thanks again. -- 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.
[gmx-users] Coul. Recip. in Logfile for Classical Ewald
I'm doing a classical Ewald simulation with GROMACS (obviously I should be using something other than Ewald in my simulations like PME, but I am just trying to understand the concept and write some analysis code.). In the logfile does Coul. Recip. include the self correction (or any other kind of correction)? I'm having a little trouble seeing where the specific number comes from and am trying to understand. Adding up the kspace contribution (from GROMACS) and self contribution (my own calculation) doesn't seem to get me the number from the logfile. I know I'm missing something. As an example I ran 33 SPC waters in a 1 x 1 x 1 box with cutoffs at 0.4 (this is just a small quick simulation to get some numbers for this purpose). Again this is classical Ewald, fourierspacing is the default 0.12, and ewald-rtol is the default 1e-5. I added the following line to src/mdlib/ewald.c just before return energy; in the do_ewald function and recompiled : printf(%5.6f\n,energy); This prints out the k-space contribution to the electrostatic energy at each step. As an example, at step 0 this it printed out 1008.472290 (kJ/mol). After getting this I calculated the self contribution as follows. The logfile says that 1/beta (the Gaussian width) is 0.128065 nm, so beta = 7.808535 for this simulation. There are 33 water oxygens with a charge of -0.82 and 66 water hydrogens with a charge of 0.41. The following equation for the self term comes from section 4.9.1 of the manual (f = 138.935485): -f * beta / sqrt(pi) * [ (33)(-0.82)^2 + (66)(0.41)^2 ] = -20372.33 kJ/mol The logfile states for step 0 that Coulomb (Recip.) is -1.23120e+03 kJ/mol, but this does not equal the total of the k-space and self correction terms: 1008.5 + -20372.3 = -19363.8 I appreciate anybody's help with understanding what I'm missing here in understanding how GROMACS calculates the self correction or if Coul. Recip. is something else. Thanks, Wes Barnett -- 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.
[gmx-users] Отв: Отв: GROM (.mdp, .itp, .top) and .pdb Editor with Syntax Highlighting
Hi Alexander, I've updated the Source Code, now it's fixed. Hovakim среда, 3 сентября 2014 21:53 Александр Селютин saga1...@gmail.com писал(а): Thanks! Now it's all right. When I run binary, I lose row where you say that you use 64 bin. Some time ago, I had similar idea, but I wanted to write extension to geany, Very useful idea is the right column with documentation! I test program. I see some strange things. In the mdb files after zoom and unzoom the format is changed to bad. -- С уважением, Александр Селютин -- 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.
Re: [gmx-users] Moving part # of -noappend
On 9/3/14, 3:39 PM, Johnny Lu wrote: it gives #abc.part0001.xyz.1# and then #abc.part0001.xyz.2#. I moved all files that starts with #. Hope that works. If a simulation is actively running, it does not need the files from any previous parts. When starting a continuation run, you need the checkpoint file from the previous run and nothing else if using -noappend, which appears to be the case here. Anything that is #file# is a backup of a previous run and is never used, but indicates the multiple runs tried to produce the same output files. What that means depends on what you've been doing in the working directory (i.e. previous failed attempts, etc). -Justin On Wed, Sep 3, 2014 at 1:48 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. When gromacs is working on abc.part0010.trr, is it ok to move every file called abc.partDEFG.xyz where DEFG is less than 0010 to another place? And, after that, will gromacs make a new file called abc.part0011.trr instead of another abc.part0001.trr ? (will the part # reset to 0001 if I move some files away?) I want to keep track of the order of the parts, after I move them away. Thanks again. -- == 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.
Re: [gmx-users] Constraint and Temperature Drop in NVE
Hi, It's impossible to say anything in the absence of a full description of the system and .mdp file - expecting good conservation can be a fool's errand. You could a) investigate the effect of time step on the difference in the observed temperature b) investigate the effect of the restraint strength constant on the temperature difference (it could be too large for the time step) c) try double precision (to see if the drift is intrinsic or due to accumulated rounding imprecision) d) assess which of the approximations you are making (drift from finite time step/model/implementation, static point charges, broken ergodicity, etc.) dominates the quality of your model physics. And consider that the measurement of temperature from momentum (as in GROMACS) is intrinsically flawed - see https://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf Mark On Wed, Sep 3, 2014 at 6:21 PM, Johnny Lu johnny.lu...@gmail.com wrote: I try the following: 0. Minimization 1. NVT (100,000 steps of 2fs, 300K) 2. NPT (100,000 steps of 2fs, 300K, V-rescale thermostat) 3. NPT (5000 steps of 2fs, 308K, V-rescale thermostat) 4. 9 x NVE (each 32768 steps of 0.75 fs) 5. go to step 3. I plan to get rid of the first of nine NVE steps, as an NVE equilibration step. At 0.75 fs, the total energy drop was about 0.03% per NVE step. Will that be fine? I am a bit worry that step 3 is too short. I pick 308K because last time when I choose 300K for step 3, step 4 drops to 292 K. I hope that the NVE will be about 300K. May be I should look at the .edr file of step 3. Thanks. On Wed, Sep 3, 2014 at 11:54 AM, Johnny Lu johnny.lu...@gmail.com wrote: reading this post in maillist again: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071225.html I think that is exactly the same problem. On Wed, Sep 3, 2014 at 10:24 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run NVE (0.5fs timesteps) with a harmonic restraint with force constant 4184kJ/mol rad^2, the temperature then fluctuate around 292 K ( http://oi60.tinypic.com/sni5at.jpg) in gromacs 4.6.6. When I instead run NVE with same setting except without the constraint after the two equilibration steps, the temperature stays around 300K. What is the cause of this drop of temperature to 292K? Thanks again. -- 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. -- 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.
Re: [gmx-users] Coul. Recip. in Logfile for Classical Ewald
Hi, In the group cut-off scheme, Coul Recip also contains exclusions for (e.g.) atoms in the central cell that share bonds, which are computed in gmxlib/ewald_util.c. You would need to compare with a run without bonds, or do some more printf. Mark On Wed, Sep 3, 2014 at 7:53 PM, Barnett, James W. jbarn...@tulane.edu wrote: I'm doing a classical Ewald simulation with GROMACS (obviously I should be using something other than Ewald in my simulations like PME, but I am just trying to understand the concept and write some analysis code.). In the logfile does Coul. Recip. include the self correction (or any other kind of correction)? I'm having a little trouble seeing where the specific number comes from and am trying to understand. Adding up the kspace contribution (from GROMACS) and self contribution (my own calculation) doesn't seem to get me the number from the logfile. I know I'm missing something. As an example I ran 33 SPC waters in a 1 x 1 x 1 box with cutoffs at 0.4 (this is just a small quick simulation to get some numbers for this purpose). Again this is classical Ewald, fourierspacing is the default 0.12, and ewald-rtol is the default 1e-5. I added the following line to src/mdlib/ewald.c just before return energy; in the do_ewald function and recompiled : printf(%5.6f\n,energy); This prints out the k-space contribution to the electrostatic energy at each step. As an example, at step 0 this it printed out 1008.472290 (kJ/mol). After getting this I calculated the self contribution as follows. The logfile says that 1/beta (the Gaussian width) is 0.128065 nm, so beta = 7.808535 for this simulation. There are 33 water oxygens with a charge of -0.82 and 66 water hydrogens with a charge of 0.41. The following equation for the self term comes from section 4.9.1 of the manual (f = 138.935485): -f * beta / sqrt(pi) * [ (33)(-0.82)^2 + (66)(0.41)^2 ] = -20372.33 kJ/mol The logfile states for step 0 that Coulomb (Recip.) is -1.23120e+03 kJ/mol, but this does not equal the total of the k-space and self correction terms: 1008.5 + -20372.3 = -19363.8 I appreciate anybody's help with understanding what I'm missing here in understanding how GROMACS calculates the self correction or if Coul. Recip. is something else. Thanks, Wes Barnett -- 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. -- 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.
Re: [gmx-users] g_select syntax
Dear Teemu, Thank you for your explanation. Now I understand why the first selection gives more residues as it's simply a superset of the second selection. I just realized to accomplish what I initially want, i.e., to obtain the residue index list of LIPID whose center of mass is within 1.0 nm of the surface of protein, I just need group LIPID and res_com within 1.0 of group PROTEIN and g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx -oi index.dat -seltype res_com -selrpos atom Again, I am a bit confused by that it seems the sole function of -seltype res_com is outputting residue index instead of atom index. If I use -seltype atom instead, g_select will return all the corresponding atoms in the residues selected by the selection just above. What frustrates me most is I can't find a flag to be used in selection.dat to let g_select output residue index, not atom index. Best Regards, Bin -- 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.
Re: [gmx-users] Configuration bug preventing GROMACS 5.0 build with Intel compiler?
Hi, I'm not aware of an intrinsic problem with GROMACS and icc 14 - that icc version + CUDA 5.5 + OpenMPI compiles and passes tests (with a million warnings presumably from the wrong CUDA version for icc, which normally seems to be fine in practice). IntelMPI is not often tested with GROMACS, so I would experiment with taking it and CUDA out of the mix and observing how your mileage varies. Frankly, gcc will do just as well or slightly better... You should be able to hack out the erroneous detection by using cmake -Disfinite_compile_ok=0 etc. but I would guess that the fault here is in some wrapper compiler not propagating the inner failure correctly - all CMake can do is take the return value from the compiler. Mark On Wed, Sep 3, 2014 at 7:00 PM, Paul Caheny paul.cah...@uk.fujitsu.com wrote: Hi All, I'm attempting to compile GROMACS 5.0 (as downloaded from the tarball available here: http://www.gromacs.org/Downloads) with Intel Compiler version 14 and Intel MPI version 5 without success. I'm also compiling the CUDA functionality (with CUDA 6.5) but CUDA/MPI functionality doesn't seem to be related to the compilation problem I'm seeing. I'm using CMAKE 3.0.1 which I compiled myself from source with the same Intel 14 compiler. Here is the version info: icc --version icc (ICC) 14.0.3 20140422 Copyright (C) 1985-2014 Intel Corporation. All rights reserved. icpc --version icpc (ICC) 14.0.3 20140422 Copyright (C) 1985-2014 Intel Corporation. All rights reserved. mpirun --version Intel(R) MPI Library for Linux* OS, Version 5.0 Build 20140605 Copyright (C) 2003-2014, Intel Corporation. All rights reserved. I'm compiling like so: module load compiler/intel/14.0/3.174 module load mpi/intel/5.0/0.028 tar -zxvf gromacs-5.0.tar.gz cd gromacs-5.0 mkdir build cd build ../../../CMAKE/cmake-3.0.1_intel14.0/bin/cmake .. \ -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc \ -DGMX_MPI=on -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/app/libraries/cuda/6.5/sb \ -DCUDA_HOST_COMPILER=/app/compilers/intel/ 14.0.3.174/composer_xe_2013_sp1.3.174/bin/intel64/icpc \ -DCUDA_VERBOSE_BUILD=ON -DCUDA_VER=6.5 -DCUDA_INSTALL_PATH=/app/libraries/cuda/6.5/sb \ -DCMAKE_INSTALL_PREFIX=../../../G2/install \ -DGMX_FFT_LIBRARY=mkl \ -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_VERBOSE_MAKEFILE=ON make make install During install I see the following: file INSTALL cannot find /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/bin/gmx_mpi. Going backwards through the compilation I first see multiple instances of undefined references to _finite and _aligned_free like this one during link: /app/libraries/impi/5.0.0.028/intel64/bin/mpiicpc-mavx -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd1782 -ip -funroll-all-loops -alias-const -ansi-alias -O3 -DNDEBUG -mkl=sequential CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs_mpi.so.0.0.0 -openmp ../../lib/libgpu_utils.a ../../lib/libnbnxn_cuda.a ../../lib/libcuda_tools.a /app/libraries/cuda/6.5/sb/lib64/libcudart.so -ldl -lrt -lm -lz -Wl,-rpath,/home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/build/lib:/app/libraries/cuda/6.5/sb/lib64 ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `_finite' ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `_aligned_free' ...and earlier during compilation: /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/src/gromacs/math/utilities.c(731): warning #266: function _finite declared implicitly returnval = _finite(x); /home/paul.caheny/ISV/FY14Q2/GROMACS/G2/gromacs-5.0/src/gromacs/utility/smalloc.c(359): warning #266: function _aligned_free declared implicitly _aligned_free(free); This seems to be related to the CMAKE configuration successfully finding functions that don't exist on my platform, in particular from: -- Checking for isfinite -- Performing Test isfinite_compile_ok -- Performing Test isfinite_compile_ok - Success -- Checking for isfinite - yes -- Checking for _isfinite -- Performing Test _isfinite_compile_ok -- Performing Test _isfinite_compile_ok - Success -- Checking for _isfinite - yes -- Checking for _finite -- Performing Test _finite_compile_ok -- Performing Test _finite_compile_ok - Success -- Checking for _finite - yes -- Looking for _aligned_malloc -- Looking for _aligned_malloc - found According to build/CMakeFiles/CMakeOutput.log and CMakeError.log all the above checks pass, yet in CMakeOutput.log all except the first check (isfinite) are logged as having undefined references, yet the check still reports success. This is the just the output for _finite_compile_ok but the _isfinite_compile_ok and _aligned_malloc follow a similar pattern: Performing C SOURCE FILE Test _finite_compile_ok succeded with the following
Re: [gmx-users] adding ions in the genion for multimeric proteins
Hi, Use genion -neutral and let gromacs do that hard work. Regards, On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh ambargrom...@gmail.com wrote: Dear users, My protein is a trimer and I want to run md : on binding of a peptide (chain-D) to this trimer (chain-ABC). Therefore, I have four chains. So, when I create topol.top file using pdb2gmx it automatically divide the topology in four *.itp files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp so, in time of running genion command its required to mention the number of ions to neutralize the protein. Now, each of the protein monomer contains net charge of 2 (qtot) in chain A, B and C. D-peptide have final qtot as 0. Now the question is : Where can I get final qtot for whole system? Is it like that: I have to just sum up all three (2+2+2) and write -nn 6 in genion command ? Or the final qtot value is written in somewhere else in some file, which I missed? I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much Sincerely Nil -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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.
Re: [gmx-users] adding ions in the genion for multimeric proteins
When you bundle up the system run file (.tpr), using gmx grompp, to pass to gmx genion, it will list in the terminal output the net charge of the entire system. Additionally, you could simply use the -neutral option and not specify the number of ions required, the script will work that out for you. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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.
[gmx-users] Regarding gromacs installation
Hi I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS. During installation there was no error. But i didnt get information like Gromacs has been successfully installed. When i use pdb2gmx or mdrun commands it is showing command not found. I dont know what is the problem and how should i rectify it. Please help me to solve this. -- With regards, Sathya.B -- 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.
Re: [gmx-users] Regarding gromacs installation
Follow this link http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.11._Getting_access_to_GROMACS_after_installation Chandan On Thu, Sep 4, 2014 at 10:32 AM, Sathya bti027.2...@gmail.com wrote: Hi I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS. During installation there was no error. But i didnt get information like Gromacs has been successfully installed. When i use pdb2gmx or mdrun commands it is showing command not found. I dont know what is the problem and how should i rectify it. Please help me to solve this. -- With regards, Sathya.B -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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.
