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.
[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] Query about a simple MD with constant electric field
Dear Erik, yes, that was the problem. I set comm-mode = none and now it works also without PME and for non-neutral systems Thank you very much Ivan On 2016-03-14 10:50, Erik Marklund wrote: Dear Ivan, It works also without PME and for non-neutral systems. What are your COM-removal settings? They can certainly mess up an accelerating system. Kind regards, Erik On 10 Mar 2016, at 10:33, Ivan Gladich <iglad...@sissa.it> wrote: Dear Prof. Spoel first of all thank you for your reply. 1) No, I did not get any warning about PME and charge system, just a note NOTE 4 [file topol.top, line 23]: System has non-zero total charge: 1.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer 2) I tried the simulation with a plain cut-off scheme and no PME and but still my positive ion moves with constant velocity. At the link below you can see my files, the coord.xvg and the veloc.xvg for the coordinates and the velocity of my ion https://goo.gl/Q0pyR9 3) Following your suggestions, I have also tried an MD using PME and two ions of opposite charge. The two ions were placed at about 2.5 nm distance, interacting only through electrostatic and with a cut-off of 0.9 nm. Interestingly, here the behavior seems correct with the velocity that grows linearly with time (see velocBr.xvg and velocNa.xvg attached in the link below) https://goo.gl/TDM0lZ Thus my new questionDoes the electric field in Gromacs works only with PME and neutral system? Thank you very very much for your help Ivan On 2016-03-09 20:10, David van der Spoel wrote: On 09/03/16 11:48, Ivan Gladich wrote: Dear Gromacs users I am doing a very simple MD with a constant electric field of 1 V/nm along the positive z-direction in a system containing only one Na+ ion, starting from rest. The ion is not coupled to the thermostat and it is placed in a box of 4 nm* 4nm * 16 nm, in the X,Y,and Z direction respectively. I would expect my ion accelerating along the positive Z-direction with constant acceleration. However my ion starts to move in the positive Z-direction but with constant velocity for all my 1 ns MD. Do I do something really wrong? Yes :). I guess you got at least a warning from grompp, right? About using a charged system with PME. If you have a net charge in the system PME compensates for it by applying a homogeneous charge distribution with the opposite sign. This can give interesting results. You could try using a cut-off instead if you just have one particle. Or use an ion pair. I am using gromacs 5.1.1 in double precision Thanks for any possible help Below my inputs Ivan ### conf.gro ### Gyas ROwers Mature At Cryogenic Speed 1 2183Na Na 6545 3.014 0.540 8.909 4.0 4.0 16.0 ## topol.top # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon Na11 79.901. A0.385 0.0022 [ moleculetype ] ; molname nrexcl Na 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1.0 [ system ] THE-BEST [ molecules ] ; Compoundnmols Na 1 # grompp.mdp # title = Na+Electric ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; = 1000ps dt = 0.001 ; 1 fs ; Output control nstxout = 0 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 5000; save energies every 1 ps nstlog = 5000; update log file every 1 ps nstxtcout = 1000; xtc compressed trajectory output every 1 ps ; Neighborsearching cutoff-scheme = group ;Verlet ns_type = grid ; search neighboring grid cells nstlist = 1; 20 fs, largely irrelevant with Verlet rlist = 0.9 rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 0.9 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = no ; ; Pressure coupling pcoupl = no; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= no ; ; Velocity generation gen_vel = no ;Electric E-x = 0 0 0 E-y = 0 0 0 E-z = 1 1 0 : 1 V nm-1 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.
Re: [gmx-users] Query about a simple MD with constant electric field
Dear Prof. Spoel first of all thank you for your reply. 1) No, I did not get any warning about PME and charge system, just a note NOTE 4 [file topol.top, line 23]: System has non-zero total charge: 1.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer 2) I tried the simulation with a plain cut-off scheme and no PME and but still my positive ion moves with constant velocity. At the link below you can see my files, the coord.xvg and the veloc.xvg for the coordinates and the velocity of my ion https://goo.gl/Q0pyR9 3) Following your suggestions, I have also tried an MD using PME and two ions of opposite charge. The two ions were placed at about 2.5 nm distance, interacting only through electrostatic and with a cut-off of 0.9 nm. Interestingly, here the behavior seems correct with the velocity that grows linearly with time (see velocBr.xvg and velocNa.xvg attached in the link below) https://goo.gl/TDM0lZ Thus my new questionDoes the electric field in Gromacs works only with PME and neutral system? Thank you very very much for your help Ivan On 2016-03-09 20:10, David van der Spoel wrote: On 09/03/16 11:48, Ivan Gladich wrote: Dear Gromacs users I am doing a very simple MD with a constant electric field of 1 V/nm along the positive z-direction in a system containing only one Na+ ion, starting from rest. The ion is not coupled to the thermostat and it is placed in a box of 4 nm* 4nm * 16 nm, in the X,Y,and Z direction respectively. I would expect my ion accelerating along the positive Z-direction with constant acceleration. However my ion starts to move in the positive Z-direction but with constant velocity for all my 1 ns MD. Do I do something really wrong? Yes :). I guess you got at least a warning from grompp, right? About using a charged system with PME. If you have a net charge in the system PME compensates for it by applying a homogeneous charge distribution with the opposite sign. This can give interesting results. You could try using a cut-off instead if you just have one particle. Or use an ion pair. I am using gromacs 5.1.1 in double precision Thanks for any possible help Below my inputs Ivan ### conf.gro ### Gyas ROwers Mature At Cryogenic Speed 1 2183Na Na 6545 3.014 0.540 8.909 4.0 4.0 16.0 ## topol.top # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon Na11 79.901. A0.385 0.0022 [ moleculetype ] ; molname nrexcl Na 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1.0 [ system ] THE-BEST [ molecules ] ; Compoundnmols Na 1 # grompp.mdp # title = Na+Electric ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; = 1000ps dt = 0.001 ; 1 fs ; Output control nstxout = 0 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 5000; save energies every 1 ps nstlog = 5000; update log file every 1 ps nstxtcout = 1000; xtc compressed trajectory output every 1 ps ; Neighborsearching cutoff-scheme = group ;Verlet ns_type = grid ; search neighboring grid cells nstlist = 1; 20 fs, largely irrelevant with Verlet rlist = 0.9 rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 0.9 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = no ; ; Pressure coupling pcoupl = no; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= no ; ; Velocity generation gen_vel = no ;Electric E-x = 0 0 0 E-y = 0 0 0 E-z = 1 1 0 : 1 V nm-1 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Query about a simple MD with constant electric field
Dear Gromacs users I am doing a very simple MD with a constant electric field of 1 V/nm along the positive z-direction in a system containing only one Na+ ion, starting from rest. The ion is not coupled to the thermostat and it is placed in a box of 4 nm* 4nm * 16 nm, in the X,Y,and Z direction respectively. I would expect my ion accelerating along the positive Z-direction with constant acceleration. However my ion starts to move in the positive Z-direction but with constant velocity for all my 1 ns MD. Do I do something really wrong? I am using gromacs 5.1.1 in double precision Thanks for any possible help Below my inputs Ivan ### conf.gro ### Gyas ROwers Mature At Cryogenic Speed 1 2183Na Na 6545 3.014 0.540 8.909 4.0 4.0 16.0 ## topol.top # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon Na11 79.901. A0.385 0.0022 [ moleculetype ] ; molname nrexcl Na 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1.0 [ system ] THE-BEST [ molecules ] ; Compoundnmols Na 1 # grompp.mdp # title = Na+Electric ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; = 1000ps dt = 0.001 ; 1 fs ; Output control nstxout = 0 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 5000; save energies every 1 ps nstlog = 5000; update log file every 1 ps nstxtcout = 1000; xtc compressed trajectory output every 1 ps ; Neighborsearching cutoff-scheme = group ;Verlet ns_type = grid ; search neighboring grid cells nstlist = 1; 20 fs, largely irrelevant with Verlet rlist = 0.9 rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 0.9 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = no ; ; Pressure coupling pcoupl = no; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= no ; ; Velocity generation gen_vel = no ;Electric E-x = 0 0 0 E-y = 0 0 0 E-z = 1 1 0 : 1 V nm-1 -- 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] Simulations with Verlet scheme, virtual sites and heterogeneous systems
Dear Mark thanks for your reply. As you suggested, I will try with the version 5.0.4 and I will test the setup this water model with Verlet and in bulk water. I will keep you posted Ivan On 04/27/2015 03:04 PM, Mark Abraham wrote: On Mon, Apr 27, 2015 at 12:26 PM, Ivan Gladich iglad...@sissa.it wrote: Dear Gromacs users, I am experiencing a strange behavior using Verlet-cutoff scheme in combination with a water model with virtual sites. I am simulating an ice slab with NE6 water model. NE6 water model is used for simulation of ice and it consists of 3 atom sites and 3 virtual sites. My system has two vacuum interfaces as drawn below. ||- vacuum | ice | vacuum | | --- My simulation run at 240 K and, at this temperature, my ice should not melt (for this water model Tm=289 K). Using a group scheme , my ice remains stable over 10 ns cutoff-scheme = group ns_type = grid nstlist = 1 rlist = 1 pbc= xyz rcoulomb = 1.0 vdw-type = Cut-Off rvdw = 1.0 * **On the contrary*, using a Verlet cut-off scheme cutoff-scheme = Verlet ns_type = grid nstlist = 10 pbc = xyz vdw-type = Cut-Off rvdw = 1.0 I start to observe that 1) sometimes my ice suddenly (not in a realist way) melts after ~7 ns and my simulation crashes OR 2) some particle are kicked out with high velocity and my run crashes with this message --- Program mdrun_4_7_gpu_s, VERSION 4.6.7 Source code file: /home/igladich/opt/gromacs-4.6.7/src/mdlib/pme.c, line: 851 Fatal error: 2 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am uploading the temperature profile and the *.mdp file at http://goo.gl/0zfqfe So, my questions concern the Verlet scheme 1) Can this scheme properly work in the presence of an heterogeneous system as mine (with an interface on vacuum)? Most certainly - we use it for a water droplet in vacuum falling onto a surface, for example. There's nothing about the implementation that cares about heterogeneity. 2) Can the problem be the virtual sites in my water models? Because I saw, running grompp the following note... NOTE 2 [file grompp-RUN-NE6-4_7.mdp]: There are 5760 non-linear virtual site constructions. Their contribution to the energy drift is approximated. In most cases this does not affect the energy drift significantly. Perhaps. How well does your model actually do at reproducing (say) bulk water properties under the various conditions? I can't recall if there's been a relevant vsites bug fix since 4.6, but you could try 5.0.4 also. Mark 3) Is there a way to go around this issue? With GPU+Verlet and I doing ~110 ns/day while, with group+CPU 33 ns/day Thanks for any possible help or suggestions Sincerely Ivan -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail:iglad...@sissa.it web page:http://people.sissa.it/~igladich/ -- 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. -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail: iglad...@sissa.it web page: http://people.sissa.it/~igladich/ -- 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] Simulations with Verlet scheme, virtual sites and heterogeneous systems
Dear Gromacs users, I am experiencing a strange behavior using Verlet-cutoff scheme in combination with a water model with virtual sites. I am simulating an ice slab with NE6 water model. NE6 water model is used for simulation of ice and it consists of 3 atom sites and 3 virtual sites. My system has two vacuum interfaces as drawn below. ||- vacuum | ice | vacuum | | --- My simulation run at 240 K and, at this temperature, my ice should not melt (for this water model Tm=289 K). Using a group scheme , my ice remains stable over 10 ns cutoff-scheme = group ns_type = grid nstlist = 1 rlist = 1 pbc= xyz rcoulomb = 1.0 vdw-type = Cut-Off rvdw = 1.0 * **On the contrary*, using a Verlet cut-off scheme cutoff-scheme = Verlet ns_type = grid nstlist = 10 pbc = xyz vdw-type = Cut-Off rvdw = 1.0 I start to observe that 1) sometimes my ice suddenly (not in a realist way) melts after ~7 ns and my simulation crashes OR 2) some particle are kicked out with high velocity and my run crashes with this message --- Program mdrun_4_7_gpu_s, VERSION 4.6.7 Source code file: /home/igladich/opt/gromacs-4.6.7/src/mdlib/pme.c, line: 851 Fatal error: 2 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am uploading the temperature profile and the *.mdp file at http://goo.gl/0zfqfe So, my questions concern the Verlet scheme 1) Can this scheme properly work in the presence of an heterogeneous system as mine (with an interface on vacuum)? 2) Can the problem be the virtual sites in my water models? Because I saw, running grompp the following note... NOTE 2 [file grompp-RUN-NE6-4_7.mdp]: There are 5760 non-linear virtual site constructions. Their contribution to the energy drift is approximated. In most cases this does not affect the energy drift significantly. 3) Is there a way to go around this issue? With GPU+Verlet and I doing ~110 ns/day while, with group+CPU 33 ns/day Thanks for any possible help or suggestions Sincerely Ivan -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail:iglad...@sissa.it web page:http://people.sissa.it/~igladich/ -- 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 the Pi-Pi and pi-cation interaction
Hi, to the best of my knowledge, Molecular Dynamics is not the best way to study system stabilized by Pi-Pi or Pi-Cataion interaction. However,in MD people usually overpolarized C-C and C-H bonds to increase the quadrupole interactions, and thus, mimic the Pi-Pi interaction See http://pubs.acs.org/doi/pdf/10.1021/jp408977b or http://pubs.rsc.org/en/content/articlelanding/2006/cp/b610253k#!divAbstract In conclusion (and in my opinion), you case use MD but be careful and test your Force field... Ivan On 2014-10-30 05:55, rama david wrote: Dear Friends, I search the archive to find the answer of my question but I did not get satisfied answer so I am putting the question in forum. One of them is as http://comments.gmane.org/gmane.science.biology.gromacs.user/51771 I want to study the MD simulation of Ligand and Receptor that is stabilize by Pi-Pi and pi-cation interaction 1. Is it right to say the Pi-Pi and pi-cation interaction can be studied by Moleculardynamics?? 2. Which force field I have to use ?? 3. In the analysis tools I found that no direct tools can do this directly. How to do this analysis I am looking forward for reply. With best regards, -- 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 the Pi-Pi and pi-cation interaction
On 2014-10-30 13:10, Justin Lemkul wrote: On 10/30/14 4:57 AM, Ivan Gladich wrote: Hi, to the best of my knowledge, Molecular Dynamics is not the best way to study system stabilized by Pi-Pi or Pi-Cataion interaction. However,in MD people usually overpolarized C-C and C-H bonds to increase the quadrupole interactions, and thus, mimic the Pi-Pi interaction See http://pubs.acs.org/doi/pdf/10.1021/jp408977b or http://pubs.rsc.org/en/content/articlelanding/2006/cp/b610253k#!divAbstract In conclusion (and in my opinion), you case use MD but be careful and test your Force field... Wouldn't this increase in polarization along these bonds require reparametrization of bonded interactions, as well? Everything is interrelated. Even if you get the quadrupole moment better, I would think there are potential issues with the bonded parameters. I guess your relative energies show that the approach is OK, but I would imagine doing this in some force fields would have big implications for the integrity of the model. I perfectly agree with you.. Indeed, we increased the polarization with a small scaling up of the charges. As you said, scaling too much you get in troubles. Scaling the charges helps the force field but it does not solve the problem. For example, even with this trick, you cannot get a perfect pi-stacking in MD ,as shown in the first paper for Naphthalene, but you get a parallel displaced dimer (Figure 6D). As I said, MD is not the best way to study these kind of systems... depends on what you need and the accuracy that you want .. Best Ivan Apologies if any more details described in the second article; our university does not have access to that journal so I am only reading the JPCA article. -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] About pdb2gmx and cyclic peptides
Dear all, I am trying to build a cyclic peptide of 12 aminoacids using pdb2gmx. Searching on the web I found that is not very straightforward without editing the topology and the .gro file https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html The problem is that I have thousand of structures and so I need to do it iteratively. I am wondering if in the newer versions of gromacs the problem has been addressed and solved. Thanks for any possible advice Ivan -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail: iglad...@sissa.it web page: http://people.sissa.it/~igladich/ -- 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] Since nstlist has no effect on the accuracy
Preso appuntamento per sabato mattina...di al papa' che si tenga libero!!! Ivan On 02/06/2014 11:09 AM, Szilárd Páll wrote: PS: The buffer is automatically calculated based on the verlet-buffer-drift set in the mdp file, for more details see the appendix of http://dx.doi.org/10.1016/j.cpc.2013.06.003. -- Szilárd On Thu, Feb 6, 2014 at 11:04 AM, Szilárd Páll pall.szil...@gmail.com wrote: Exactly. The penalty of large nstlist is large buffer (rlist), but up to 40-50 with CPUs and up to 100 with GPUs is quite realistic. Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in the mdp. From 5.0 there will be a command line option. Cheers, -- Szilárd On Thu, Feb 6, 2014 at 2:29 AM, yunshi11 . yunsh...@gmail.com wrote: In a MD run with Verlet cutoff scheme, can I set nstlist as large as possible? Like 100 or 1000? Thanks, Yun -- 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. -- -- Ivan Gladich, Ph.D. Research Assistant International School for Advanced Studies (SISSA) Via Bonomea 265, I-34136, Trieste, Italy Room: 331 Tel: +390403787335 e-mail: iglad...@sissa.it web page: http://people.sissa.it/~igladich/ -- 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.
