[gmx-users] To invoke GPU in gromacs version 4.6.4
i am trying to invoke GPU for my final mdrun step using the command mdrun -v -deffnm md -gup_id Got the following : GPU ID string set, but mdrun was compiled without GPU support. I have also included cutoff-scheme = Verlet in the md.mdp file. Kindly help me to troubleshoot this issue. Thanks Shalini.M -- 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] 100-quartz force field for GROMACS using CGenFF
Dear Justin, thank you for your prompt answer. I will contact you off-list. Best Ivan On 2017-03-05 17:14, Justin Lemkul wrote: On 3/5/17 6:56 AM, Ivan Gladich wrote: Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force field parameters and structure are available in CHARMM (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk, E. and MacKerell, Jr., A.D. "Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface," Journal of Physcial Chemistry B 110: 2782-2792, 2006. Since I am not familiar with CHARMM force field (and crystal simulations as well), my plan was to create the FF in CHARMM and then convert it to GMX format. I copied the quartz (100) structure reported in the paper above, converting it in .mol2 format, adding PBC information (see mol2 attached below). Then I tried using CHARMM General Force Field (CGenFF) program (https://cgenff.paramchem.org) uploading my .mol2 file. If I understand correctly, the quartz parameters reported in the paper above should be present in CGenFF program. However, I am getting error of the type: "Now processing molecule Q100 ... attype warning: element not supported;skipped molecule." The parameters you need are not part of CGenFF at all. They're CHARMM force field parameters and are distinct from CGenFF. They're in the "silicates" subdirectory of the CHARMM toppar files available from the link you quote above. Since I read from this mailing list that some of you currently use CGenFF, I would like to ask whether some of you have some advise on how to get this force field for this structure running in GROAMCS, using CGenFF or any other alternative way. This will require additional force field files (those found in "silicates") to be converted to GROMACS format. Contact me off-list if you need help doing this; there are various niche parts of the CHARMM force field that I haven't converted simply because no one has needed them and I don't have test cases for them. I don't know anything about such structures, so the subsequent application of the parameters is something you'll have to figure out, likely by constructing a topology using gmx x2top. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] NPT equilibration without pbc
Thanks Alex for the suggestion!! On 5 March 2017 at 01:49, Alex wrote: > I looked at that paper and there are no attempts to simulate liquid-gas > equilibrium at normal atmospheric pressure. That aside, what the authors > did instead is actually pretty mind-boggling: they replaced the droplet > with a cylinder by making the system periodic in the out-of-plane direction. > > This mailing list is probably not a great place for me to state my opinion > on this (terrible) paper, but one can indeed do what the authors did. Just > keep in mind that this is no longer a droplet, because the surface not > facing the substrate has been removed. > > However, the good news is that you can indeed (partially) simulate > atmospheric pressure this way. To do this in Gromacs, simply use > 'pcoupltype = semiisotropic' and supply a very low compressibility value in > the in-plane direction. > > Alex > > > > On 3/5/2017 12:27 AM, Rajorshi Paul wrote: > >> Thanks for your input. I am studying how a nano droplet spreads on a >> substrate. I have created a four atomic layer thick FCC lattice surface on >> which I have introduced water molecules. The entire system is placed >> inside >> a box of dimensions 15 nm X 15 nm X 10 nm. The system is similar to the >> one >> used in the following article: >> https://www.cambridge.org/core/journals/journal-of-fluid- >> mechanics/article/div-classtitlea-molecular-view-of-tanneran >> daposs-law-molecular-dynamics-simulations-of-droplet- >> spreadingdiv/E4C863EE2CFE2E17B343D0AAE85D2BB4 >> I am interested in simulating normal atmospheric conditions in my study. >> >> On 4 March 2017 at 23:30, Alex wrote: >> >> Once again, please describe your system in more detail, because this isn't >>> about Gromacs (which will correctly refuse pressure coupling for a >>> finite, >>> deep-nanoscale system). It is about the meaning of where pressure comes >>> from in simulations and in reality. >>> >>> In a realistic system "1 bar" would come from the air environment + any >>> water evaporation in equilibrium with the liquid phase of the droplet. >>> Even >>> if you made your surface periodic, pressure coupling would have nothing >>> to >>> do with your finite droplet -- it would be in vacuum. Consider this work, >>> for instance: http://www.nature.com/nmat/jou >>> rnal/v15/n1/abs/nmat4449.html >>> >>> Alex >>> >>> >>> >>> On 3/4/2017 11:17 PM, Rajorshi Paul wrote: >>> >>> Hi Alex, Like I mentioned, my system consists of a water nano drop on a substrate. I need my system to be at 1 bar and 298 K. Without pressure coupling, I am unable to set the pressure to be at 1 bar. On 4 March 2017 at 22:18, Alex wrote: 1. Could you please provide a physical equivalent of a non-periodic NPT > system? > 2. Why can't you turn off the barostat, like GMX is asking? > > Alex > > > On 3/4/2017 8:40 PM, Rajorshi Paul wrote: > > I am trying to simulate water nano droplet spreading on an FCC crystal > >> substrate. I have not implemented periodic boundary conditions as my >> system >> is non-periodic. But when I tried to equilibrate my system in NPT >> ensemble, >> the program gives me a warning that I should set pressure coupling as >> "no". >> Is it possible to run NPT equilibration in non-periodic system? >> >> Thanks! >> >> Raj. >> >> -- >> > 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. > -- *Rajorshi Paul * B.Tech. (Hons.), Gold Medallist (IIT Kharagpur) First year Master of Science student Mechanical Engineering Department University of Alberta Edmonton, Alberta Canada. Office: NINT 6-17 Email: rajorshipaul.iit...@gmail.com Phone: +1 780 782 4744 -- Gromacs Users mailing list * Please search the archive at http://www.g
Re: [gmx-users] 100-quartz force field for GROMACS using CGenFF
On 3/5/17 6:56 AM, Ivan Gladich wrote: Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force field parameters and structure are available in CHARMM (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk, E. and MacKerell, Jr., A.D. "Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface," Journal of Physcial Chemistry B 110: 2782-2792, 2006. Since I am not familiar with CHARMM force field (and crystal simulations as well), my plan was to create the FF in CHARMM and then convert it to GMX format. I copied the quartz (100) structure reported in the paper above, converting it in .mol2 format, adding PBC information (see mol2 attached below). Then I tried using CHARMM General Force Field (CGenFF) program (https://cgenff.paramchem.org) uploading my .mol2 file. If I understand correctly, the quartz parameters reported in the paper above should be present in CGenFF program. However, I am getting error of the type: "Now processing molecule Q100 ... attype warning: element not supported;skipped molecule." The parameters you need are not part of CGenFF at all. They're CHARMM force field parameters and are distinct from CGenFF. They're in the "silicates" subdirectory of the CHARMM toppar files available from the link you quote above. Since I read from this mailing list that some of you currently use CGenFF, I would like to ask whether some of you have some advise on how to get this force field for this structure running in GROAMCS, using CGenFF or any other alternative way. This will require additional force field files (those found in "silicates") to be converted to GROMACS format. Contact me off-list if you need help doing this; there are various niche parts of the CHARMM force field that I haven't converted simply because no one has needed them and I don't have test cases for them. I don't know anything about such structures, so the subsequent application of the parameters is something you'll have to figure out, likely by constructing a topology using gmx x2top. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] membrane proteins simulation
On 3/5/17 1:44 AM, Negar Parvizi wrote: Dear all users, I am new in membrane proteins simulation. I want to simulate a membrane protein that it is a part of a large protein and has a big extracellular part.Here is my question: is it ok, I just simulate the membrane part even it is a part of a large protein? and if the answer is yes, what is the best expiation for it ? That depends on the biological function of the protein and what is known about how the different domains may interact. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] UMBRELLA SAMPLING
On 3/4/17 9:24 AM, Subashini .K wrote: Hi gromacs users, I want to calculate delta G for protein ligand binding. Had run the umbrella pulling simulation for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website, Bevenlab). But, after running the perl script (perl distances.pl), did not obtain any distance on the right column (summary_distances.dat). It was blank. (1) Had applied the position restrain of the protein during NPT equilibration. (2) During puling simulation, again applied the restrain on the protein. Is it correct? How to rectify the mistake and proceed in the right direction? The script from the tutorial is designed for use with the tutorial and therefore makes assumptions about the groups that are in the index file. Invoke gmx distance yourself so you can see how to properly use it, then adjust the script as needed. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] 100-quartz force field for GROMACS using CGenFF
Dear all, I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated interface using GROAMCS. Force field parameters and structure are available in CHARMM (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk, E. and MacKerell, Jr., A.D. "Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface," Journal of Physcial Chemistry B 110: 2782-2792, 2006. Since I am not familiar with CHARMM force field (and crystal simulations as well), my plan was to create the FF in CHARMM and then convert it to GMX format. I copied the quartz (100) structure reported in the paper above, converting it in .mol2 format, adding PBC information (see mol2 attached below). Then I tried using CHARMM General Force Field (CGenFF) program (https://cgenff.paramchem.org) uploading my .mol2 file. If I understand correctly, the quartz parameters reported in the paper above should be present in CGenFF program. However, I am getting error of the type: "Now processing molecule Q100 ... attype warning: element not supported;skipped molecule." Since I read from this mailing list that some of you currently use CGenFF, I would like to ask whether some of you have some advise on how to get this force field for this structure running in GROAMCS, using CGenFF or any other alternative way. Thank you very much for any possible help or hint. Ivan @MOLECULE Q100 43 403 SMALL USER_CHARGES @ATOM 1 Si 0.17001.0500 13.0600 Si1 Si 0. 2 Si1 0.17003.5000 17.3100 Si1 Si 0. 3 Si2 0.17001.0500 21.5600 Si1 Si 0. 4 Si3 0.17003.5000 25.8100 Si1 Si 0. 5 O 0.80001.5400 11.6500 O 2 O 0. 6 O1 0.80003.9900 15.9000 O 2 O 0. 7 O2 0.80001.5400 20.1500 O 2 O 0. 8 O3 0.80003.9900 24.4100 O 2 O 0. 9 O4 4.40002.0500 13.5000 O 2 O 0. 10 O5 4.40004.5000 17.7500 O 2 O 0. 11 O6 4.40002.0500 22.0100 O 2 O 0. 12 O7 4.40004.5000 26.2600 O 2 O 0. 13 O8 4.94004.5000 12.7700 O 2 O 0. 14 O9 4.94002.0500 17.0300 O 2 O 0. 15 O10 4.94004.5000 21.2800 O 2 O 0. 16 O11 4.94002.0500 25.5300 O 2 O 0. 17 O12 1.34000.9400 14.1400 O 2 O 0. 18 O13 1.34003.3900 18.3900 O 2 O 0. 19 O14 1.34000.9400 22.6400 O 2 O 0. 20 O15 1.34003.3900 26.9000 O 2 O 0. 21 Si4 1.97002.4200 11.0100 Si1 Si 0. 22 Si5 1.9700 -0.0400 15.2600 Si1 Si 0. 23 Si6 1.97002.4200 19.5200 Si1 Si 0. 24 Si7 1.9700 -0.0400 23.7700 Si1 Si 0. 25 Si8 1.97002.4200 28.0200 Si1 Si 0. 26 Si9 3.77003.5000 13.2200 Si1 Si 0. 27 Si103.77001.0500 17.4700 Si1 Si 0. 28 Si113.77003.5000 21.7200 Si1 Si 0. 29 Si123.77001.0500 25.9800 Si1 Si 0. 30 O16 2.60003.3900 12.1400 O 2 O 0. 31 O17 2.60000.9400 16.3900 O 2 O 0. 32 O18 2.60003.3900 20.6400 O 2 O 0. 33 O19 2.60000.9400 24.8900 O 2 O 0. 34 O20 3.14003.9900 14.6200 O 2 O 0. 35 O21 3.14001.5400 18.8800 O 2 O 0. 36 O22 3.14003.9900 23.1300 O 2 O 0. 37 O23 3.14001.5400 27.3800 O 2 O 0. 38 H 1.34003.39009.8900 H 3 H 0. 39 H1 3.14001.5400 10.3700 H 3 H 0. 40 O24 0.80001.5400 28.6600 O 2 O 0. 41 O25 2.60003.3900 29.1400 O 2 O 0. 42 H2 0.80001.5400 29.7600 H 3 H 0. 43 H3 2.60003.3900 30.2400 H 3 H 0. @BOND 115 1 21 17 1 3
Re: [gmx-users] NPT equilibration without pbc
I looked at that paper and there are no attempts to simulate liquid-gas equilibrium at normal atmospheric pressure. That aside, what the authors did instead is actually pretty mind-boggling: they replaced the droplet with a cylinder by making the system periodic in the out-of-plane direction. This mailing list is probably not a great place for me to state my opinion on this (terrible) paper, but one can indeed do what the authors did. Just keep in mind that this is no longer a droplet, because the surface not facing the substrate has been removed. However, the good news is that you can indeed (partially) simulate atmospheric pressure this way. To do this in Gromacs, simply use 'pcoupltype = semiisotropic' and supply a very low compressibility value in the in-plane direction. Alex On 3/5/2017 12:27 AM, Rajorshi Paul wrote: Thanks for your input. I am studying how a nano droplet spreads on a substrate. I have created a four atomic layer thick FCC lattice surface on which I have introduced water molecules. The entire system is placed inside a box of dimensions 15 nm X 15 nm X 10 nm. The system is similar to the one used in the following article: https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/div-classtitlea-molecular-view-of-tannerandaposs-law-molecular-dynamics-simulations-of-droplet-spreadingdiv/E4C863EE2CFE2E17B343D0AAE85D2BB4 I am interested in simulating normal atmospheric conditions in my study. On 4 March 2017 at 23:30, Alex wrote: Once again, please describe your system in more detail, because this isn't about Gromacs (which will correctly refuse pressure coupling for a finite, deep-nanoscale system). It is about the meaning of where pressure comes from in simulations and in reality. In a realistic system "1 bar" would come from the air environment + any water evaporation in equilibrium with the liquid phase of the droplet. Even if you made your surface periodic, pressure coupling would have nothing to do with your finite droplet -- it would be in vacuum. Consider this work, for instance: http://www.nature.com/nmat/journal/v15/n1/abs/nmat4449.html Alex On 3/4/2017 11:17 PM, Rajorshi Paul wrote: Hi Alex, Like I mentioned, my system consists of a water nano drop on a substrate. I need my system to be at 1 bar and 298 K. Without pressure coupling, I am unable to set the pressure to be at 1 bar. On 4 March 2017 at 22:18, Alex wrote: 1. Could you please provide a physical equivalent of a non-periodic NPT system? 2. Why can't you turn off the barostat, like GMX is asking? Alex On 3/4/2017 8:40 PM, Rajorshi Paul wrote: I am trying to simulate water nano droplet spreading on an FCC crystal substrate. I have not implemented periodic boundary conditions as my system is non-periodic. But when I tried to equilibrate my system in NPT ensemble, the program gives me a warning that I should set pressure coupling as "no". Is it possible to run NPT equilibration in non-periodic system? Thanks! Raj. -- 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.
