Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
I have tried the same with Berendsen and it still crashes. I have seen this happen before in some other versions compatibility too (I have an old post about it in the mailing list). Thanks for the response! On Thu, Jun 27, 2013 at 3:21 PM, Justin Lemkul wrote: > > > On 6/27/13 3:16 PM, Sapna Sarupria wrote: > >> Thanks Justin for the response. I thought of that too but was not sure if >> that could alone be attributed to the crash. There is no obvious reason >> why >> it should happen given Gromacs has typically been quite stable. This is >> quite a straightforward system...but perhaps it is the version. I am able >> to run other simulations in this version with similar set up and >> therefore, >> I wonder what is going wrong. >> >> > Without an actual backtrace from gdb, there's not much to go on, but then > too, the development team isn't going to try to fix anything about 4.5.4 > that presumably has already been fixed. The most obvious culprit in the > .mdp file below is the combination of velocity generation and Nose-Hoover; > it's not a very stable combination. > > -Justin > > >> On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/27/13 2:30 PM, sarupria wrote: >>> >>> Hello all, >>>> >>>> I have a naphthalene + water system which I want to run a NPT simulation >>>> of. >>>> The system has been energy mininimized. When I run the NPT simulation >>>> using >>>> gromacs 4.5.5 the simulation runs fine, but when I attempt to run the >>>> same >>>> simulation using 4.5.4 it crashes with lincs error. We have tried >>>> various >>>> things like energy minimizing multiple times using 4.5.4 but it still >>>> crashes. I have also changed the thermostat and barostat to Berendsen, >>>> the >>>> problem persists. >>>> >>>> Has anything changed between the two versions that could lead to this >>>> trouble? I am pasted the mdp file below and also the last few lines of >>>> the >>>> error message I get from Gromacs 4.5.4. >>>> >>>> >>>> Well, according to the release notes (http://www.gromacs.org/About_** >>> ** <http://www.gromacs.org/About_**> >>> Gromacs/Release_Notes/Versions_4.5.x<http://www.** >>> gromacs.org/About_Gromacs/**Release_Notes/Versions_4.5.x<http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x> >>> >)**, >>> in version 4.5.5: >>> >>> "Many small fixes which avoid termination with fatal errors or crashes in >>> mdrun and tools." >>> >>> Small bugs are constantly getting fixed. I see no compelling reason to >>> use an outdated version (4.5.4) when a slightly less outdated version >>> (4.5.5) works correctly. >>> >>> -Justin >>> >>> >>> Thanks for your help. >>> >>>> Sapna >>>> >>>> MDP FILE * >>>> title = NPH + water ; a string >>>> dt = 0.002; time step >>>> nsteps = 1250 ; number of steps >>>> comm-grps = system >>>> comm-mode = Linear >>>> nstcomm = 10 ; reset c.o.m. motion >>>> nstxout = 000 ; write coords >>>> nstvout = 000 ; write velocities >>>> nstlog = 2500 ; print to logfile >>>> nstenergy = 500 ; print energies >>>> xtc_grps= System >>>> nstxtcout = 1000 >>>> nstlist = 10 ; update pairlist >>>> ns_type = grid ; pairlist method >>>> coulombtype = PME >>>> rvdw= 1.00 ; cut-off for vdw >>>> rcoulomb= 1.00 ; cut-off for coulomb >>>> rlist = 1.00 ; cut-off for coulomb >>>> Tcoupl = Nose-Hoover >>>> ref_t = 280.0 >>>> tc-grps = System >>>> tau_t = 0.5 >>>> DispCorr= EnerPres ; long range correction >>>> gen_vel = yes
Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
>> *** End Error Message * >> >> >> >> -- >> View this message in context: http://gromacs.5086.x6.nabble.** >> com/Gromacs-4-5-4-and-Gromacs-**4-5-5-give-different-results-** >> tp5009424.html<http://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> >> > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Sapna Sarupria Assistant Professor, Department of Chemical and Biomolecular Engineering 128 Earle Hall (206 S Palmetto Blvd) Clemson University Clemson, SC 29678 Phone: 864-656-3258 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Water spreading on graphene!
Dear David, I apologize for the confusion. There are no partial charges on the graphene sheet . The only interactions between the sheet and water are from VdW interactions. To give some background: We were initially simulating graphene oxide with water which has partial charges. Then to test the effect of oxygens we retained the carbons and their partial charges, and simulated the system. As expected it was hydrophilic. Then we turned off all the partial charges to obtain a graphene sheet and tested the system. Unexpectedly, we still saw the drop spreading. That is how the whole mystery originated. I hope this clarifies things. Again, there are no partial charges on the graphene sheet. Sapna On Sun, Apr 21, 2013 at 1:23 PM, David van der Spoel wrote: > On 2013-04-21 18:25, Sapna Sarupria wrote: > >> Dear David and all, >> >> >> Thanks for the suggestions! >> >> I did increase the box size to twice that of the sheet dimensions. The >> sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 >> nm^3 >> box with the droplet size of about 5 nm (4142 water molecules). I still >> see >> the droplet spreading. >> >> I will check the energies and also attempt the simulation with the cut-off >> distances. May be that will help. >> >> However, in a silica surface with no surface charges the drop remains a >> drop (as expected). I use the same mdp files for both the simulations. >> >> You did not explain the charges on graphene. > > > Sapna >> >> >> On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel >> wrote: >> >> On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: >>> >>> Yes, the water droplet should remain a droplet on graphene. >>>> >>>> Since you have a droplet, I assume you have much vacuum in the system. I >>>> would not use PME for such system, but would rather "compensate" it by >>>> using larger cutoffs. >>>> >>>> It could be an artifact if the box dimension is small compared to the >>>> >>> droplet (less than double the droplet size, make it at least three times >>> the droplet). In principle PME should work though. Check the energy >>> before >>> and after the droplet spreads to see whether the energy goes down. >>> >>> >>> >>> If you need a simple advice, it is -- enlarge the box to avoid any >>> >>>> interactions, which you would not have had in real experiment. >>>> >>>> Indeed. >>> >>> >>> >>> I also expect a specific behavior, if your droplet is very small. >>>> >>>> Maybe, I would simulate this system without PBC at all. >>>> >>>> >>>> Dr. Vitaly Chaban >>>> >>>> >>>> >>>> >>>> >>>> > > -- > 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 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Water spreading on graphene!
Dear David and all, Thanks for the suggestions! I did increase the box size to twice that of the sheet dimensions. The sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 nm^3 box with the droplet size of about 5 nm (4142 water molecules). I still see the droplet spreading. I will check the energies and also attempt the simulation with the cut-off distances. May be that will help. However, in a silica surface with no surface charges the drop remains a drop (as expected). I use the same mdp files for both the simulations. Sapna On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel wrote: > On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: > >> Yes, the water droplet should remain a droplet on graphene. >> >> Since you have a droplet, I assume you have much vacuum in the system. I >> would not use PME for such system, but would rather "compensate" it by >> using larger cutoffs. >> >> It could be an artifact if the box dimension is small compared to the > droplet (less than double the droplet size, make it at least three times > the droplet). In principle PME should work though. Check the energy before > and after the droplet spreads to see whether the energy goes down. > > > > If you need a simple advice, it is -- enlarge the box to avoid any >> interactions, which you would not have had in real experiment. >> > Indeed. > > > >> I also expect a specific behavior, if your droplet is very small. >> >> Maybe, I would simulate this system without PBC at all. >> >> >> Dr. Vitaly Chaban >> >> >> >> >> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Water spreading on graphene!
Dear David, Vitaly and all, Thanks for the thoughts/comments. There are no partial charges on the carbons in this sheet. (Sorry if there was any confusion about this). I used gromacs_4.5.5 version for these simulations. I also did increase the graphene sheet size to 10 nm x 10 nm and the box size to have 4142 water molecules. Initially the drop is placed about 3-4 nm away from the graphene sheet. In 600 ps the drop moves towards the sheet (forming something that looks like a pillar of water) and begins to spread on the sheet. The setup itself is placed in a 20 nm x 20 nm x 20 nm box. So both big sheet, and big box do not seem to help. The interesting part is I have another set of simulations with silica surface. The partial charges are turned off to make it hydrophobic. In this case the droplet remains a droplet. The mdp files are the same - I am using PME and NVT system with the drop and sheet coupled to different thermostats. The silica surface is frozen (so t_ref = 0 for the sheet). I have tested this system for gromacs 4.0.5, and 4.5.5. In both cases it remains a droplet. The only difference in the two is that in case of silica surface the surface is periodic, while graphene is a finite size sheet. Does this make such a big difference? Thoughts, comments, suggestions welcome! thanks all, Sapna On Sun, Apr 21, 2013 at 6:39 AM, Dr. Vitaly Chaban wrote: > Yes, the water droplet should remain a droplet on graphene. > > Since you have a droplet, I assume you have much vacuum in the system. I > would not use PME for such system, but would rather "compensate" it by > using larger cutoffs. > > If you need a simple advice, it is -- enlarge the box to avoid any > interactions, which you would not have had in real experiment. > > I also expect a specific behavior, if your droplet is very small. > > Maybe, I would simulate this system without PBC at all. > > > Dr. Vitaly Chaban > > > > > > > > > I have a graphene like surface (carbons on a hexagonal lattice with zero > > partial charges and some LJ parameters) with a drop of water placed on > it. > > In principle, this is a hydrophobic surface and the drop should remain a > > droplet on it. However, surprisingly I am seeing that the drop is > spreading > > within a 1 ns of the simulation. In the past I have done some similar > > simulations (with a different structure but basically zero partial charge > > surface and LJ) on which the drop remains a drop. > > > > Does any body have any ideas of what I may be doing wrong? Pasted below > is > > my mdp and top file. Briefly, I am doing NVT simulation, PME for > > electrostatics, TIP3P water model, the surface is frozen and > intra-surface > > interactions are excluded, the cut-off distances are 1 nm, velocity > rescale > > thermostat (I tried both with the entire system coupled to the same > > thermostat and with sheet and water being coupled to different > > thermostats). > > Any suggestions are welcome. > > > > My analysis suggests this comes from the long range electrostatics > because > > we have tested the same thing in LAMMPS. When we turn off PPPM and use > > cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the > > software) we don't see the drop spreading. > > > > I have done so many simulations and to have this problem stumps me!! > Thanks > > for being helpful always. > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hbond Shake and Gromacs Version Related
That is a very valid point, Mark! and very well said indeed. Yes, you are absolutely correct that we were in a rush to get to the "equilibrium" point but it had to be pushed gently. Thanks, Sapna On Mon, Aug 20, 2012 at 7:29 PM, Mark Abraham wrote: > On 21/08/2012 9:02 AM, Sapna Sarupria wrote: >> >> Thanks Mark. >> >> I also discovered that if I set the value of nstpcoule = 1 explicitly >> in my mdp file, it runs with the newer version of Gromacs 4.5.5 which >> was not the case earlier. > > > Yes, default behaviour of this kind of thing has varied over time. Again, > small changes in inputs can have big changes in output. To insulate yourself > from such things, equilibrate gently. > > >> Can you tell me what this variable does exactly? > > > Manual 7.3.15 :-) > > >> Will your suggestion >> that the initial setup might be faulty still be valid? > > > I didn't say the starting configuration was faulty - just that you were > likely being too rough with it. The children's swings at the park are > designed to be pushed along an equilibrium plane, but if you start the swing > off that plane and maybe push in a strange direction, don't be surprised if > the child cries :-) > > Mark > > >> >> Thanks, >> Sapna >> >> On Mon, Aug 20, 2012 at 6:54 PM, Mark Abraham >> wrote: >>> >>> On 21/08/2012 8:45 AM, Sapna Sarupria wrote: >>>> >>>> Hello All, >>>> >>>> I have been having rather bizarre experience with Gromacs and was >>>> wondering if any one can shed some light on what is happening. I am >>>> running simulations of a hydrate + water system (think of hydrate as >>>> ice if you are not familiar with them). So basically I have a simple >>>> solid+liquid system. The system is minimized. The water model I am >>>> using is TIP4P/2005. Now when I run the simulation using grompp and >>>> mdrun both from Gromacs 4.5.5, my system crashes and writes out >>>> step*.pdb files. This I know happens when the system is exploding or >>>> something however, I do not see an obvious reason for this. >>>> However, if I compile the tpr file with older Gromacs version 4.0.5 >>>> and then use mdrun from 4.5.5 to run the simulation, my simulation >>>> proceeds just finethe way I expect it to. >>> >>> >>> Minor differences in how things are constructed can have big effects on >>> numerical integration. MD is chaotic. >>> >>> >>>> Can anyone tell me what might be happening here. I have pasted my mdp >>>> file below. I think this might be related to the constraint algorithm >>>> but I have no idea how to fix it. I have tried using Lincs instead of >>>> Shake and that also gives the same outcome. Runs with Gromacs 4.0.5 >>>> (i.e. grompp using 4.0.5 and mdrun using 4.5.5) and fails with 4.5.5 >>>> (both grompp and mdrun using 4.5.5). >>>> >>>> Please let me know if you need any further information and thanks a >>>> lot for your help. Any insight will be helpful. >>>> >>>> BEGIN MDP FILE ### >>>> title = s1-Hydrate melting simulation >>>> dt = 0.002; time step >>>> nsteps = 5000; number of steps >>>> nstcomm = 10 ; reset c.o.m. motion >>>> nstxout = 7500 ; write coords >>>> nstvout = 7500 ; write velocities >>>> nstlog = 25000; print to logfile >>>> nstenergy = 250 ; print energies >>>> xtc_grps= System >>>> nstxtcout = 25 >>>> nstlist = 10 ; update pairlist >>>> ns_type = grid ; pairlist method >>>> coulombtype = PME >>>> rvdw= 1.20 ; cut-off for vdw >>>> rcoulomb= 1.20 ; cut-off for coulomb >>>> rlist = 1.20 ; cut-off for coulomb >>>> Tcoupl = Nose-Hoover >>>> ref_t = 200.0 >>>> tc-grps = System >>>> tau_t = 0.5 >>>> Pcoupl = Parrinello-Rahman >>>> Pcoupltype = sem
Re: [gmx-users] Hbond Shake and Gromacs Version Related
Thanks Mark. I also discovered that if I set the value of nstpcoule = 1 explicitly in my mdp file, it runs with the newer version of Gromacs 4.5.5 which was not the case earlier. Can you tell me what this variable does exactly? Will your suggestion that the initial setup might be faulty still be valid? Thanks, Sapna On Mon, Aug 20, 2012 at 6:54 PM, Mark Abraham wrote: > On 21/08/2012 8:45 AM, Sapna Sarupria wrote: >> >> Hello All, >> >> I have been having rather bizarre experience with Gromacs and was >> wondering if any one can shed some light on what is happening. I am >> running simulations of a hydrate + water system (think of hydrate as >> ice if you are not familiar with them). So basically I have a simple >> solid+liquid system. The system is minimized. The water model I am >> using is TIP4P/2005. Now when I run the simulation using grompp and >> mdrun both from Gromacs 4.5.5, my system crashes and writes out >> step*.pdb files. This I know happens when the system is exploding or >> something however, I do not see an obvious reason for this. >> However, if I compile the tpr file with older Gromacs version 4.0.5 >> and then use mdrun from 4.5.5 to run the simulation, my simulation >> proceeds just finethe way I expect it to. > > > Minor differences in how things are constructed can have big effects on > numerical integration. MD is chaotic. > > >> Can anyone tell me what might be happening here. I have pasted my mdp >> file below. I think this might be related to the constraint algorithm >> but I have no idea how to fix it. I have tried using Lincs instead of >> Shake and that also gives the same outcome. Runs with Gromacs 4.0.5 >> (i.e. grompp using 4.0.5 and mdrun using 4.5.5) and fails with 4.5.5 >> (both grompp and mdrun using 4.5.5). >> >> Please let me know if you need any further information and thanks a >> lot for your help. Any insight will be helpful. >> >> BEGIN MDP FILE ### >> title = s1-Hydrate melting simulation >> dt = 0.002; time step >> nsteps = 5000; number of steps >> nstcomm = 10 ; reset c.o.m. motion >> nstxout = 7500 ; write coords >> nstvout = 7500 ; write velocities >> nstlog = 25000; print to logfile >> nstenergy = 250 ; print energies >> xtc_grps= System >> nstxtcout = 25 >> nstlist = 10 ; update pairlist >> ns_type = grid ; pairlist method >> coulombtype = PME >> rvdw= 1.20 ; cut-off for vdw >> rcoulomb= 1.20 ; cut-off for coulomb >> rlist = 1.20 ; cut-off for coulomb >> Tcoupl = Nose-Hoover >> ref_t = 200.0 >> tc-grps = System >> tau_t = 0.5 >> Pcoupl = Parrinello-Rahman >> Pcoupltype = semiisotropic; pressure geometry >> tau_p = 1.0 1.0; p-coupoling time >> compressibility = 4.5e-5 4.5e-5 ; compressibility >> ref_p = 100.0 100.0; ref pressure >> DispCorr= EnerPres ; long range correction >> gen_vel = yes ; generate init. vel >> gen_temp= 200 ; init. temp. >> gen_seed= 98247; random seed >> constraints = hbonds; constraining bonds with H >> constraint_algorithm = shake >> > > As you will see in > http://www.gromacs.org/Documentation/Terminology/Blowing_Up, the problem is > usually not with the constraints, but they're the first thing to show > deviant behaviour. Your use of T and P coupling algorithms is likely > inappropriate for equilibration given your starting point. Equilibrating > initially with Berendsen and/or a small time step will likely move you to a > point where you can switch to the algorithms that produce proper ensembles. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list
[gmx-users] Hbond Shake and Gromacs Version Related
Hello All, I have been having rather bizarre experience with Gromacs and was wondering if any one can shed some light on what is happening. I am running simulations of a hydrate + water system (think of hydrate as ice if you are not familiar with them). So basically I have a simple solid+liquid system. The system is minimized. The water model I am using is TIP4P/2005. Now when I run the simulation using grompp and mdrun both from Gromacs 4.5.5, my system crashes and writes out step*.pdb files. This I know happens when the system is exploding or something however, I do not see an obvious reason for this. However, if I compile the tpr file with older Gromacs version 4.0.5 and then use mdrun from 4.5.5 to run the simulation, my simulation proceeds just finethe way I expect it to. Can anyone tell me what might be happening here. I have pasted my mdp file below. I think this might be related to the constraint algorithm but I have no idea how to fix it. I have tried using Lincs instead of Shake and that also gives the same outcome. Runs with Gromacs 4.0.5 (i.e. grompp using 4.0.5 and mdrun using 4.5.5) and fails with 4.5.5 (both grompp and mdrun using 4.5.5). Please let me know if you need any further information and thanks a lot for your help. Any insight will be helpful. BEGIN MDP FILE ### title = s1-Hydrate melting simulation dt = 0.002; time step nsteps = 5000; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 7500 ; write coords nstvout = 7500 ; write velocities nstlog = 25000; print to logfile nstenergy = 250 ; print energies xtc_grps= System nstxtcout = 25 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.20 ; cut-off for vdw rcoulomb= 1.20 ; cut-off for coulomb rlist = 1.20 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 200.0 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p = 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 100.0 100.0; ref pressure DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 200 ; init. temp. gen_seed= 98247; random seed constraints = hbonds; constraining bonds with H constraint_algorithm = shake END MDP FILE ### Thanks very much, Sapna -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4
Hi Itamar and Mark, The error message is pasted below. I tried both running minimization and then running the MD; and using a configuration from a previous simulation (that was run using Gromacs 4.0.5). In both these case the simulations are crashing. The error message is similar. Mark, Yes there is no reason as such to have TIP and SOL defined but it is for the purpose of my simulations. It helps me differentiate between water phases at the beginning of the simulation (SOL is in solid and TIP is in liquid phase). Indeed, they are exactly the same, as they are supposed to be. I also tried using the Berendsen coupling for both temperature and pressure, but the simulations still crash. Like I mentioned, all of these simulations work perfectly in 4.0.5 Gromacs version with Nose-Hoover and PR starting from the exact same configuration (except initial velocity) that I am using in 4.5 version. Thank you all for your suggestions and help. Sapna. Error Message from Gromacs starting mdrun 'Hydrate with cages filled with carbon dioxide' 1500 steps, 3.0 ps. step 0Inner product between old and new vector <= 0.0! constraint #1 atoms 25869 and 25871 Wrote pdb files with previous and current coordinates Inner product between old and new vector <= 0.0! constraint #1 atoms 145 and 147 Wrote pdb files with previous and current coordinates Segmentation fault @ On Wed, Oct 19, 2011 at 6:19 PM, Mark Abraham wrote: > On 20/10/2011 8:40 AM, Sapna Sarupria wrote: > > Hello, > > I did change nsttcouple and nstpcouple but the simulations that run in > 4.0.5 are still crashing in 4.5.4. I think it is related to constraints but > I am unable to figure out exactly what is different. I have pasted both my > topology and mdp (updated for 4.5.4) files. Any ideas? I have read through > the manual and it seems like the mdp files does not need any changes, but > perhaps I am missing something. > > > P-R P-coupling is not well-suited to equilibration if you are not close to > equilibrium. Since you are generating velocities, you are likely not close > to equilibrium. > > I don't see that it is causing a problem, but there is no reason to have > both SOL and TIP molecule type. They're identical. > > Mark > > > > Thank you for your help! > > Sincerely, > Sapna > > MDP File > title = 100% occupancy CO2 hydrate ; a string > cpp = /lib/cpp ; c-preprocessor > integrator= md > dt = 0.002; time step > nsteps = 1500 ; number of steps > nstcomm = 10 ; reset c.o.m. motion > nstxout = ; write coords > nstvout = ; write velocities > nstlog = 25000; print to logfile > nstenergy = 500 ; print energies > xtc_grps = OW_HW1_HW2_CO2 > nstxtcout= 1000 > nstlist = 10 ; update pairlist > ns_type= grid ; pairlist method > coulombtype= PME > rvdw= 1.2 ; cut-off for vdw > rcoulomb = 1.2 ; cut-off for coulomb > rlist = 1.2 ; cut-off for coulomb > DispCorr = EnerPres > Tcoupl = Nose-Hoover > ref_t = 270 > tc-grps = System > tau_t = 0.5 > nsttcouple = 1 > Pcoupl = Parrinello-Rahman > Pcoupltype= semiisotropic; pressure geometry > tau_p = 1.0 1.0; p-coupoling time > compressibility = 4.5e-5 4.5e-5 ; compressibility > ref_p = 30.5 30.5 ; ref pressure > nstpcouple = 1 > gen_vel = yes ; generate initial vel > gen_temp= 260 ; initial temperature > gen_seed = 372340 ; random seed > constraint_algorithm = shake > constraints = all-bonds > end MDP File > > Topology file > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 no 1.0 1.0 > > [ atomtypes ] > ; name mass chargeptype sigma epsilon > ; Water parameters are those of Vega TIP4P/Ice Model > OWT4 15.9994 0.A 0.31668 0.882164429 > HW1.008 0.5897A 0.000 0.000 > MW0.000 -1.1794V 0.000 0.000 > &g
Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4
a 3 1 2 1 0.50 4 1 2 1 -0.086327900 5 1 2 1 1.086327913 [ exclusions ] 3 4 5 4 5 3 5 4 3 [ system ] Hydrate with cages filled with carbon dioxide [ molecules ] SOL2944 CO2512 TIP3641 End topology file On Wed, Oct 19, 2011 at 7:17 AM, Sapna Sarupria wrote: > Dear Itamar and Justin, > > Thank you for your responses. I will make the changes to the mdp files and > see how easy or hard it is to make the shift from 4.0.5 to 4.5. > > Sincerely, > Sapna > > > On Tue, Oct 18, 2011 at 10:28 PM, Justin A. Lemkul wrote: > >> >> >> Itamar Kass wrote: >> >>> Hi Sapna, >>> >>> It is a good question, but such of personal preferences. I found out >>> that my simulations tend to crash more often when I am using 4.5.5. It might >>> be the General-reaction -field I use or something else, I am not sure. Also, >>> it seems I will not gain much from upgrading, so I stick to 4.0.7. >>> >>> >> The general instabilities result from tweaks to the handling of >> temperature and pressure coupling. Simply setting nsttcouple and nstpcouple >> to 1 during the initial equilibration seems to give stable systems. >> >> I'd say there are many reasons for upgrading. Tons of new features, bug >> fixes, etc. But then too, that's my personal preference ;) >> >> -Justin >> >> All this is not to say that 4.5.5 is not a good simulation package. It is >>> a good and useful MD package, and I highly appreciate all the time and >>> effort put into it. >>> >>> Best, >>> Itamat >>> >>> PS, there are still people around using 3.3.3 or even 3.2.1, so I am not >>> that behind. >>> On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote: >>> >>> Dear Itamar, >>>> >>>> Thank you for your response. Why did you prefer to stick to 4.0.7? Is >>>> there something particularly difficult to transfer from 4.0.7 version to >>>> 4.5 >>>> version? >>>> >>>> Sapna >>>> >>>> On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass >>>> >>> itamar.k...@monash.edu**>> wrote: >>>> >>>>Hi Sapna, >>>> >>>>I had the same problem few weeks ago. >>>> >>>>Apparently, some parameters are different (eg. nstpcouple). >>>> >>>>Cheers, >>>>Itamar >>>> >>>>PS I found out that I prefer to stick to 4.0.7. >>>> >>>> >>>> >>>> >>>>On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: >>>> >>>> Dear All, >>>>> >>>>>I have a simulation set up for a mixture of carbon dioxide and >>>>>water system which runs perfectly on Gromacs 4.0.5 version. I >>>>>have run these simulations at different temperatures and >>>>>pressures, from the same starting configuration and the >>>>>simulation proceeds smoothly in the 4.0.5 version. However, when >>>>>I use exactly the same files to run the simulation in 4.5.4 >>>>>version, the system crashes and writes out several pdb files. I >>>>>was wondering if there is anything specific that has been changed >>>>>between the two versions. I have pasted the mdp file of the >>>>>simulations below. Any input will be much appreciated. >>>>> >>>>>MDP File >>>>>title = 100% occupancy CO2 hydrate ; a string >>>>>cpp = /lib/cpp ; c-preprocessor >>>>>dt = 0.002; time step >>>>>nsteps = 1500 ; number of steps >>>>>nstcomm = 10 ; reset c.o.m. motion >>>>>nstxout = ; write coords >>>>>nstvout = ; write velocities >>>>>nstlog = 25000; print to logfile >>>>>nstenergy = 500 ; print energies >>>>>xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 >>>>>nstlist = 10 ; update pairlist >>>>>ns_type=
Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4
Dear Itamar and Justin, Thank you for your responses. I will make the changes to the mdp files and see how easy or hard it is to make the shift from 4.0.5 to 4.5. Sincerely, Sapna On Tue, Oct 18, 2011 at 10:28 PM, Justin A. Lemkul wrote: > > > Itamar Kass wrote: > >> Hi Sapna, >> >> It is a good question, but such of personal preferences. I found out that >> my simulations tend to crash more often when I am using 4.5.5. It might be >> the General-reaction -field I use or something else, I am not sure. Also, it >> seems I will not gain much from upgrading, so I stick to 4.0.7. >> >> > The general instabilities result from tweaks to the handling of temperature > and pressure coupling. Simply setting nsttcouple and nstpcouple to 1 during > the initial equilibration seems to give stable systems. > > I'd say there are many reasons for upgrading. Tons of new features, bug > fixes, etc. But then too, that's my personal preference ;) > > -Justin > > All this is not to say that 4.5.5 is not a good simulation package. It is >> a good and useful MD package, and I highly appreciate all the time and >> effort put into it. >> >> Best, >> Itamat >> >> PS, there are still people around using 3.3.3 or even 3.2.1, so I am not >> that behind. >> On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote: >> >> Dear Itamar, >>> >>> Thank you for your response. Why did you prefer to stick to 4.0.7? Is >>> there something particularly difficult to transfer from 4.0.7 version to 4.5 >>> version? >>> >>> Sapna >>> >>> On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass >> itamar.k...@monash.edu**>> wrote: >>> >>>Hi Sapna, >>> >>>I had the same problem few weeks ago. >>> >>>Apparently, some parameters are different (eg. nstpcouple). >>> >>>Cheers, >>>Itamar >>> >>>PS I found out that I prefer to stick to 4.0.7. >>> >>> >>> >>> >>>On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: >>> >>> Dear All, >>>> >>>>I have a simulation set up for a mixture of carbon dioxide and >>>>water system which runs perfectly on Gromacs 4.0.5 version. I >>>>have run these simulations at different temperatures and >>>>pressures, from the same starting configuration and the >>>>simulation proceeds smoothly in the 4.0.5 version. However, when >>>>I use exactly the same files to run the simulation in 4.5.4 >>>>version, the system crashes and writes out several pdb files. I >>>>was wondering if there is anything specific that has been changed >>>>between the two versions. I have pasted the mdp file of the >>>>simulations below. Any input will be much appreciated. >>>> >>>>MDP File >>>>title = 100% occupancy CO2 hydrate ; a string >>>>cpp = /lib/cpp ; c-preprocessor >>>>dt = 0.002; time step >>>>nsteps = 1500 ; number of steps >>>>nstcomm = 10 ; reset c.o.m. motion >>>>nstxout = ; write coords >>>>nstvout = ; write velocities >>>>nstlog = 25000; print to logfile >>>>nstenergy = 500 ; print energies >>>>xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 >>>>nstlist = 10 ; update pairlist >>>>ns_type= grid ; pairlist method >>>>coulombtype= PME >>>>rvdw = 1.2 ; cut-off for vdw >>>>rcoulomb = 1.2 ; cut-off for coulomb >>>>rlist= 1.2 ; cut-off >>>>for coulomb >>>>DispCorr = EnerPres >>>>Tcoupl = Nose-Hoover >>>>ref_t = 270 tc-grps = System >>>>tau_t = 0.5 Pcoupl = >>>> Parrinello-Rahman >>>>Pcoupltype = semiisotropic; pressure geometry >>>>tau_p= 1.0 1.0; p
Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4
Dear Itamar, Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version? Sapna On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass wrote: > Hi Sapna, > > I had the same problem few weeks ago. > > Apparently, some parameters are different (eg. nstpcouple). > > Cheers, > Itamar > > PS I found out that I prefer to stick to 4.0.7. > > > > > On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: > > Dear All, > > I have a simulation set up for a mixture of carbon dioxide and water system > which runs perfectly on Gromacs 4.0.5 version. I have run these simulations > at different temperatures and pressures, from the same starting > configuration and the simulation proceeds smoothly in the 4.0.5 version. > However, when I use exactly the same files to run the simulation in 4.5.4 > version, the system crashes and writes out several pdb files. I was > wondering if there is anything specific that has been changed between the > two versions. I have pasted the mdp file of the simulations below. Any input > will be much appreciated. > > MDP File > > title = 100% occupancy CO2 hydrate ; a string > cpp = /lib/cpp ; c-preprocessor > dt = 0.002; time step > nsteps = 1500 ; number of steps > nstcomm = 10 ; reset c.o.m. motion > nstxout = ; write coords > nstvout = ; write velocities > nstlog = 25000; print to logfile > nstenergy = 500 ; print energies > xtc_grps = OW_HW1_HW2_CO2 > nstxtcout = 1000 > nstlist = 10 ; update pairlist > ns_type= grid ; pairlist method > coulombtype= PME > rvdw = 1.2 ; cut-off for vdw > rcoulomb = 1.2 ; cut-off for coulomb > rlist= 1.2 ; cut-off for coulomb > DispCorr = EnerPres > Tcoupl = Nose-Hoover > ref_t = 270 > tc-grps = System > tau_t = 0.5 > Pcoupl = Parrinello-Rahman > Pcoupltype = semiisotropic; pressure geometry > tau_p= 1.0 1.0; p-coupoling time > compressibility = 4.5e-5 4.5e-5 ; compressibility > ref_p = 30.5 30.5 ; ref pressure > gen_vel = yes ; generate initial vel > gen_temp = 260 ; initial temperature > gen_seed = 372340 ; random seed > constraint_algorithm = shake > constraints = all-bonds > > --- > > > Thank you, > > Sincerely, > Sapna > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > - > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > === > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs versions 4.0.5 and 4.5.4
Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated. MDP File title = 100% occupancy CO2 hydrate ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 1500 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = ; write coords nstvout = ; write velocities nstlog = 25000; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw = 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist= 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 270 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p= 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp = 260 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds --- Thank you, Sincerely, Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Implementation of Andersen Thermostat
Dear All, I was just wondering if Andersen thermostat is implemented or going to be implemented in the recent/forthcoming versions of Gromacs. Is there anyone who has done it otherwise and would be willing to share an outline of the subroutines that they modified? Thanks in advance for your help, Regards Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Wrtiing pair interaction energy on the fly
Thank you Mark for your response. I only need to double check a few things for which using generic C kernels should suffice. I need to run only 1 or 2 steps and not in parallel. Thanks again for your help. Sapna On Wed, Sep 15, 2010 at 9:43 PM, Mark Abraham wrote: > > > - Original Message - > From: sapna sarupria > Date: Thursday, September 16, 2010 1:35 > Subject: [gmx-users] Wrtiing pair interaction energy on the fly > To: Discussion list for GROMACS users > > > Dear all > > > > I understand that pair interactions in gromacs are calculated through > assembly loops. Can some one guide me to the resources using which I can > write out the interaction energy/force for each pair directly from gromacs > during the simulation (without using the rerun option). The rerun option is > especially difficult when you want pair interaction between all atoms of > one's system since one has to define that many index groups. I most cases > rerun is good, but in my case I have to test interaction between several > pairs. > > You are limited to 256 energy groups with or without using -rerun. If you > need more, then perhaps you should consider some other simulation software > that is better suited to this task. With GROMACS, you could use an > environment variable to force the use of the generic C kernels, and inside > that kernel use printf to write out the energy for each interaction. This > will be horribly slow, and will be vastly simpler if not attempted in > parallel. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Wrtiing pair interaction energy on the fly
Dear all I understand that pair interactions in gromacs are calculated through assembly loops. Can some one guide me to the resources using which I can write out the interaction energy/force for each pair directly from gromacs during the simulation (without using the rerun option). The rerun option is especially difficult when you want pair interaction between all atoms of one's system since one has to define that many index groups. I most cases rerun is good, but in my case I have to test interaction between several pairs. Thanks for your help, Regards, Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Speeding up simulation
That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is. On Wed, Aug 18, 2010 at 10:26 AM, ms wrote: > On 17/08/10 22:36, Justin A. Lemkul wrote: > > There is no way to limit PME to certain ranges. It is a method for >> solving infinite sums. Usually PME is a poor choice for in vacuo >> simulations and the like, since there's nothing to be done for most of >> the simulation box. >> > > This interests me -I've used simple cut-off for in vacuo tests, but I still > hadn't made my mind on what electrostatic model I should truly use. Do you > have any suggestion? > > thanks, > M. > > > You may want to see how others (in the literature) >> deal with droplet-type simulations. >> >> -Justin >> >> >>> Thanks for your help. >>> >>> Sapna >>> >>> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul >> <mailto:jalem...@vt.edu>> wrote: >>> >>> >>> >>> sapna sarupria wrote: >>> >>> Hi all, >>> >>> I am running (NVT) simulations of a drop of water (~5 nm in >>> radius) in a big box (~25 nm) in a box and find that the >>> simulations are rather slow. I am getting about 0.8 ns per day >>> when a simulation of bulk system of equivalent number of waters >>> will be much faster. The number of waters is ~12000. I was >>> wondering if anyone can suggest methods with which I can speed >>> up the simulations. I am using domain decomposition and >>> optimize_fft is set to yes. PME is used for the electrostatics. >>> >>> >>> I would suspect that the lag comes from a lot of unused PME >>> calculations. During your run, PME grid points will be assigned to >>> vacuum space, for which nothing needs to be done. You can check >>> imbalances and performance loss in the log file. >>> >>> -Justin >>> >>> >>> Thank you >>> >>> Sincerely >>> Sapna >>> >>> >>> -- >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> >>> -- >>> Sapna Sarupria >>> Post-doctoral Researcher >>> Princeton University >>> New Jersey 08540 >>> U.S.A. >>> >>> Life isn't about finding yourself. Life is about creating yourself. -- >>> George Bernard Shaw. >>> Dare to Dream >>> >>> >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Speeding up simulation
Hi Justin Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can. Thanks, Sapna On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul wrote: > > > sapna sarupria wrote: > >> Hi Justin >> Thanks for your response. I suspect that it is the same thing. Is there a >> way to make gromacs use PME only within a certain region of the simulation >> box? Also, how does one know how to fix the load imbalances (in this >> context)? >> > > There is no way to limit PME to certain ranges. It is a method for solving > infinite sums. Usually PME is a poor choice for in vacuo simulations and > the like, since there's nothing to be done for most of the simulation box. > You may want to see how others (in the literature) deal with droplet-type > simulations. > > -Justin > > >> Thanks for your help. >> >> Sapna >> >> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>sapna sarupria wrote: >> >>Hi all, >> >>I am running (NVT) simulations of a drop of water (~5 nm in >>radius) in a big box (~25 nm) in a box and find that the >>simulations are rather slow. I am getting about 0.8 ns per day >>when a simulation of bulk system of equivalent number of waters >>will be much faster. The number of waters is ~12000. I was >>wondering if anyone can suggest methods with which I can speed >>up the simulations. I am using domain decomposition and >>optimize_fft is set to yes. PME is used for the electrostatics. >> >> >>I would suspect that the lag comes from a lot of unused PME >>calculations. During your run, PME grid points will be assigned to >>vacuum space, for which nothing needs to be done. You can check >>imbalances and performance loss in the log file. >> >>-Justin >> >> >>Thank you >> >>Sincerely >>Sapna >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before >>posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Sapna Sarupria >> Post-doctoral Researcher >> Princeton University >> New Jersey 08540 >> U.S.A. >> >> Life isn't about finding yourself. Life is about creating yourself. -- >> George Bernard Shaw. >> Dare to Dream >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Speeding up simulation
Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul wrote: > > > sapna sarupria wrote: > >> Hi all, >> >> I am running (NVT) simulations of a drop of water (~5 nm in radius) in a >> big box (~25 nm) in a box and find that the simulations are rather slow. I >> am getting about 0.8 ns per day when a simulation of bulk system of >> equivalent number of waters will be much faster. The number of waters is >> ~12000. I was wondering if anyone can suggest methods with which I can speed >> up the simulations. I am using domain decomposition and optimize_fft is set >> to yes. PME is used for the electrostatics. >> > > I would suspect that the lag comes from a lot of unused PME calculations. > During your run, PME grid points will be assigned to vacuum space, for which > nothing needs to be done. You can check imbalances and performance loss in > the log file. > > -Justin > > >> Thank you >> >> Sincerely >> Sapna >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: NPH Simulations
Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using particle decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I currently use 16 processors for the simulation. Thank you for your help and suggestions. Sincerely Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Speeding up simulation
Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. Thank you Sincerely Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
When you run an NVT simulation the box coordinates are not written out in the edr file. You can try to extract the box information from your trajectory files. On Fri, Aug 13, 2010 at 6:42 PM, Rama G wrote: > > Thanks guys, > > Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z. > Any other way out? > > Best, > > Juju > > -- > *From:* Jussi Lehtola > *To:* gmx-users@gromacs.org > *Sent:* Fri, August 13, 2010 3:29:56 PM > > *Subject:* Re: [gmx-users] Check V for NVT > > On Fri, 13 Aug 2010 18:23:40 -0400 > "Justin A. Lemkul" wrote: > > Rama G wrote: > > > Hi Gmx users, > > > > > > I am using 4.0.X version of Gromacs and doing a NVT simulation. Now > > > I wanna check if the Volume is constant after the simulation. > > > I tried g_energy but did not find "Volume" in the pool of the > > > options. Can anyone help me? > > > > > > > Box-X, -Y, and -Z are in the .edr file. From these, you can > > calculate the volume. > > Or, you can just tell g_energy to calculate the density - if it's > constant then so is the volume... > -- > -- > Jussi Lehtola, FM, Tohtorikoulutettava > Fysiikan laitos, Helsingin Yliopisto > jussi.leht...@helsinki.fi, p. 191 50632 > -- > Mr. Jussi Lehtola, M. Sc., Doctoral Student > Department of Physics, University of Helsinki, Finland > jussi.leht...@helsinki.fi > -- > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] NPH Simulations
Hi All, I was wondering if there is a way to run simulations in the NPH ensemble in Gromacs. Does any one have experience doing this? Thank you Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?
Hi Sander That helps quite a bit. Thanks so much! Sapna On Tue, Mar 30, 2010 at 12:50 PM, Sander Pronk wrote: > There *should* be no preference, but I seem to remember that one of the > artifacts of using Ewald-style electrostatic treatment (such as PME) is that > there may be dipole-coupling between periodic images, especially if one > symmetry has already been broken. > That doesn't mean you shouldn't use PME, though: you're a long way off from > the thermodynamic limit, so you can't rely on fluctuations being slow. The > situation you're describing will always happen, and with a small number of > particles (i.e. less than you can see with the naked eye) it will happen > sooner rather than later. > > Sander > > > On Mar 30, 2010, at 18:00 , sapna sarupria wrote: > > Hi Sander > Thanks for your response. Is there then a preference for z-dimension to > expand (other than the way the system is setup in terms of semi-isotropic > coupling). Would one see an expansion in any one direction if I had the same > system setup with independent pressure coupling for each dimension > (anisotropic)? > > Thanks, > Sapna > > On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk wrote: > >> It sounds like the normal thing that would happen if you have a system >> that has no shear elastic constant, like a fluid. >> In that case, there are no restoring forces against growth of system size >> in one coordinate with a concomitant decrease in the other coordinates, so >> eventually this should happen (unless I misunderstand the nature of your >> system). >> >> Sander >> >> >> On Mar 30, 2010, at 17:47 , sapna sarupria wrote: >> >> Hello all, >> >> I have a simulation running for a hydrate (with CO2) and water in contact >> with each other. I run the simulation at 280K at which the hydrate melts and >> finally the system is just liquid water with CO2 in it. However, as the >> simulation proceeds the box begins to expand in the z-direction and >> decreases in the x-y direction considerably. Initially the box has >> 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates >> more) and is fine for another 10 ns but after that the dimensions in the x-y >> direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this >> point the simulation crashes since my cut-off distance are 1.2 nm. >> >> I am using semi-isotropic pressure coupling but the pressure in the x-y >> direction and z-direction are the same (=30.5 bar) and so is the >> compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling >> and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake >> is used to maintain their geometry. The simulation time step is 2 fs. Can >> someone tell me why such a thing happens? I have pasted my mdp file for >> completeness. I am using Gromacs 4.0.5 and I run the simulations in >> parallel using 4 processors. Values related to domain decomposition etc are >> unchanged and the default values are used. >> >> Any insights will be helpful. Thanks for the help. >> >> MDP File: >> title = CO2 hydrate + water ; a string >> cpp = /lib/cpp ; c-preprocessor >> dt = 0.002; time step >> nsteps = 2500; number of steps >> nstcomm = 10 ; reset c.o.m. motion >> nstxout = 2; write coords >> nstvout = 2; write velocities >> nstlog= 25000; print to logfile >> nstenergy = 500 ; print energies >> xtc_grps= OW_HW1_HW2_CO2 >> nstxtcout = 500 >> nstlist = 10 ; update pairlist >> ns_type = grid ; pairlist method >> coulombtype = PME >> rvdw= 1.2 ; cut-off for vdw >> rcoulomb = 1.2 ; cut-off for coulomb >> rlist = 1.2 ; cut-off for coulomb >> DispCorr = EnerPres >> Tcoupl = Nose-Hoover >> ref_t = 300 >> tc-grps = System >> tau_t = 0.5 >> Pcoupl = Parrinello-Rahman >> Pcoupltype = semiisotropic; pressure geometry >> tau_p = 1.0 1.0; p-coupling time >> compressibility = 4.5e-5 4.5e-5 ; compressibility >> ref_p
Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?
Hi Sander Thanks for your response. Is there then a preference for z-dimension to expand (other than the way the system is setup in terms of semi-isotropic coupling). Would one see an expansion in any one direction if I had the same system setup with independent pressure coupling for each dimension (anisotropic)? Thanks, Sapna On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk wrote: > It sounds like the normal thing that would happen if you have a system that > has no shear elastic constant, like a fluid. > In that case, there are no restoring forces against growth of system size > in one coordinate with a concomitant decrease in the other coordinates, so > eventually this should happen (unless I misunderstand the nature of your > system). > > Sander > > > On Mar 30, 2010, at 17:47 , sapna sarupria wrote: > > Hello all, > > I have a simulation running for a hydrate (with CO2) and water in contact > with each other. I run the simulation at 280K at which the hydrate melts and > finally the system is just liquid water with CO2 in it. However, as the > simulation proceeds the box begins to expand in the z-direction and > decreases in the x-y direction considerably. Initially the box has > 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates > more) and is fine for another 10 ns but after that the dimensions in the x-y > direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this > point the simulation crashes since my cut-off distance are 1.2 nm. > > I am using semi-isotropic pressure coupling but the pressure in the x-y > direction and z-direction are the same (=30.5 bar) and so is the > compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling > and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake > is used to maintain their geometry. The simulation time step is 2 fs. Can > someone tell me why such a thing happens? I have pasted my mdp file for > completeness. I am using Gromacs 4.0.5 and I run the simulations in > parallel using 4 processors. Values related to domain decomposition etc are > unchanged and the default values are used. > > Any insights will be helpful. Thanks for the help. > > MDP File: > title = CO2 hydrate + water ; a string > cpp = /lib/cpp ; c-preprocessor > dt = 0.002; time step > nsteps = 2500; number of steps > nstcomm = 10 ; reset c.o.m. motion > nstxout = 2; write coords > nstvout = 2; write velocities > nstlog= 25000; print to logfile > nstenergy = 500 ; print energies > xtc_grps= OW_HW1_HW2_CO2 > nstxtcout = 500 > nstlist = 10 ; update pairlist > ns_type = grid ; pairlist method > coulombtype = PME > rvdw= 1.2 ; cut-off for vdw > rcoulomb = 1.2 ; cut-off for coulomb > rlist = 1.2 ; cut-off for coulomb > DispCorr = EnerPres > Tcoupl = Nose-Hoover > ref_t = 300 > tc-grps = System > tau_t = 0.5 > Pcoupl = Parrinello-Rahman > Pcoupltype = semiisotropic; pressure geometry > tau_p = 1.0 1.0; p-coupling time > compressibility = 4.5e-5 4.5e-5 ; compressibility > ref_p = 30.5 30.5 ; ref pressure > gen_vel = yes ; generate initial vel > gen_temp= 200 ; initial temperature > gen_seed= 372340 ; random seed > constraint_algorithm = shake > constraints = all-bonds > > > > Thanks a lot > Sapna > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?
Hello all, I have a simulation running for a hydrate (with CO2) and water in contact with each other. I run the simulation at 280K at which the hydrate melts and finally the system is just liquid water with CO2 in it. However, as the simulation proceeds the box begins to expand in the z-direction and decreases in the x-y direction considerably. Initially the box has 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates more) and is fine for another 10 ns but after that the dimensions in the x-y direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this point the simulation crashes since my cut-off distance are 1.2 nm. I am using semi-isotropic pressure coupling but the pressure in the x-y direction and z-direction are the same (=30.5 bar) and so is the compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake is used to maintain their geometry. The simulation time step is 2 fs. Can someone tell me why such a thing happens? I have pasted my mdp file for completeness. I am using Gromacs 4.0.5 and I run the simulations in parallel using 4 processors. Values related to domain decomposition etc are unchanged and the default values are used. Any insights will be helpful. Thanks for the help. MDP File: title = CO2 hydrate + water ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 2500; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 2; write coords nstvout = 2; write velocities nstlog= 25000; print to logfile nstenergy = 500 ; print energies xtc_grps= OW_HW1_HW2_CO2 nstxtcout = 500 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist = 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 300 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p = 1.0 1.0; p-coupling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp= 200 ; initial temperature gen_seed= 372340 ; random seed constraint_algorithm = shake constraints = all-bonds Thanks a lot Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Semi-isotropic pressure coupling.
Hello all, I have a simulation running for a hydrate (with CO2) and water in contact with each other. I run the simulation at 280K at which the hydrate melts and finally the system is just liquid water with CO2 in it. However, as the simulation proceeds the box begins to expand in the z-direction and decreases in the x-y direction considerably. Initially the box has 4.8x4.8x9.6 nm^3 dimension. After the hydrate melts (the volume fluctuates more) and is fine for another 10 ns but after that the dimensions in the x-y direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this point the simulation crashes since my cut-off distance are 1.2 nm. I am using semi-isotropic pressure coupling but the pressure in the x-y direction and z-direction are the same (=30.5 bar) and so is the compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake is used to maintain their geometry. The simulation time step is 2 fs. Can someone tell me why such a thing happens? I have pasted my mdp file for completeness. MDP File: title = CO2 hydrate + water ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 2500; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 2; write coords nstvout = 2; write velocities nstlog= 25000; print to logfile nstenergy = 500 ; print energies xtc_grps= OW_HW1_HW2_CO2 nstxtcout = 500 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist = 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 300 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p = 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp= 200 ; initial temperature gen_seed= 372340 ; random seed constraint_algorithm = shake constraints = all-bonds Thanks a lot Sapna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using user-tables for simulations in vacuum
Hello, The simulation does not run even for one step and therefore, it is not possible for me to check any of the components such as energy, temperature etc. There is no error message except for "segmentation fault". It does the same thing if I try to energy minimize the system instead of running an MD simulation. The corresponding mdp file is pasted below: cpp= /lib/cpp constraints = none integrator = steep nstcgsteep = 500 emtol = 500.0 emstep = 0.001 vdwtype= user energygrps = POL energygrp_table = POL POL The commands I use are as follows: grompp -f em.mdp -p 25mer_wca_vac.top -c 3.5ns.gro mdrun -s topol.tpr -table table.xvg Regards Sapna On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > sapna sarupria wrote: > >> Hello, >> >> Thanks David for your response. Actually I have used the same tables for >> simulations of the polymer in water and have had no problem with them. Those >> simulations run for 4 ns without a problem. So the tables are correct and I >> am sure of that. I am not using the CVS version and so I give the energy and >> second derivative in the table. I have used user-defined tables in the past >> and so the setup is correct in terms of changing the mdp file and the top >> file. The problem seems to be more system specific (meaning vacuum) than >> user error specific. Can you suggest any other thing that may be the >> problem. >> >> Have you checked energy components, temperature etc.? > > > > Thanks a lot for your help. >> >> Regards >> Sapna >> >> >> On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel < >> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: >> >>sapna sarupria wrote: >> >> >> >>-- Forwarded message -- >>From: *sapna sarupria* <[EMAIL PROTECTED] >><mailto:[EMAIL PROTECTED]> >><mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED] >> >>> >>Date: Tue, Jul 15, 2008 at 9:16 AM >>Subject: Using user-tables for simulations in vacuum >>To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >><mailto:gmx-users@gromacs.org>>> >> >> >>Hello users, >> >>I am trying to do a simulation of a polymer chain (which is >>simply a bead of unified methane molecules) in vacuum using >>user-defined tables. The interactions are >>Weeks-Chandler-Andersen instead of Lennard-Jones. However, when >>I run the simulations, mdrun gives me a segmentation fault. When >>I run simulations for the exact same configurations without the >>tables (and therefore using VdW) the simulations run fine. In >>addition, the starting configurations were obtained after 3ns >>simulations of the polymer in water. >> >>So I was wondering if there is any issue with using user-defined >>tables with simulations in vacuum. If not do you have any idea >>what could be going wrong. >>Some details of the mdp file: >>1. pbc is turned off. >>2. there is no pressure coupling. >>3. center of mass removal is set to angular. >>4. temperature is 298 K and berendsen thermostat is used. >>5. energy groups and table are defined (correctly). >>6. the cut-offs are set to 1.0nm (box size is larger than 4 nm). >>7. no constraints are being used. >> >> >>Most obvious error source is the table itself. Do you use the CVS >>version? In that case you should provide energy and force, otherwise >>energy and second derivative. Distance units are in nm. Compare to >>existing tables in share/gromacs/top >> >> >>Thank you >> >>Regards >>Sapna >> >> >> >>--Sapna Sarupria >>Ph.D. Student - Chemical Engineering >>Rensselaer Polytechnic Institute >>Troy, New York 12180 >>U.S.A. >>Ph#: (518)276-3031 >>Life isn't about finding yourself. Life is about creating yourself. >>George Bernard Shaw. >>Dare to Dream >> >> >> >> >> >>___ >>
Re: [gmx-users] Using user-tables for simulations in vacuum
Hello, Thanks David for your response. Actually I have used the same tables for simulations of the polymer in water and have had no problem with them. Those simulations run for 4 ns without a problem. So the tables are correct and I am sure of that. I am not using the CVS version and so I give the energy and second derivative in the table. I have used user-defined tables in the past and so the setup is correct in terms of changing the mdp file and the top file. The problem seems to be more system specific (meaning vacuum) than user error specific. Can you suggest any other thing that may be the problem. Thanks a lot for your help. Regards Sapna On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > sapna sarupria wrote: > >> >> >> -- Forwarded message -- >> From: *sapna sarupria* <[EMAIL PROTECTED] > [EMAIL PROTECTED]>> >> Date: Tue, Jul 15, 2008 at 9:16 AM >> Subject: Using user-tables for simulations in vacuum >> To: Discussion list for GROMACS users > gmx-users@gromacs.org>> >> >> >> Hello users, >> >> I am trying to do a simulation of a polymer chain (which is simply a bead >> of unified methane molecules) in vacuum using user-defined tables. The >> interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However, >> when I run the simulations, mdrun gives me a segmentation fault. When I run >> simulations for the exact same configurations without the tables (and >> therefore using VdW) the simulations run fine. In addition, the starting >> configurations were obtained after 3ns simulations of the polymer in water. >> >> So I was wondering if there is any issue with using user-defined tables >> with simulations in vacuum. If not do you have any idea what could be going >> wrong. >> Some details of the mdp file: >> 1. pbc is turned off. >> 2. there is no pressure coupling. >> 3. center of mass removal is set to angular. >> 4. temperature is 298 K and berendsen thermostat is used. >> 5. energy groups and table are defined (correctly). >> 6. the cut-offs are set to 1.0nm (box size is larger than 4 nm). >> 7. no constraints are being used. >> >> > Most obvious error source is the table itself. Do you use the CVS version? > In that case you should provide energy and force, otherwise energy and > second derivative. Distance units are in nm. Compare to existing tables in > share/gromacs/top > > > Thank you >> >> Regards >> Sapna >> >> >> >> -- >> Sapna Sarupria >> Ph.D. Student - Chemical Engineering >> Rensselaer Polytechnic Institute >> Troy, New York 12180 >> U.S.A. >> Ph#: (518)276-3031 >> Life isn't about finding yourself. Life is about creating yourself. >> George Bernard Shaw. >> Dare to Dream >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Using user-tables for simulations in vacuum
-- Forwarded message -- From: sapna sarupria <[EMAIL PROTECTED]> Date: Tue, Jul 15, 2008 at 9:16 AM Subject: Using user-tables for simulations in vacuum To: Discussion list for GROMACS users Hello users, I am trying to do a simulation of a polymer chain (which is simply a bead of unified methane molecules) in vacuum using user-defined tables. The interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However, when I run the simulations, mdrun gives me a segmentation fault. When I run simulations for the exact same configurations without the tables (and therefore using VdW) the simulations run fine. In addition, the starting configurations were obtained after 3ns simulations of the polymer in water. So I was wondering if there is any issue with using user-defined tables with simulations in vacuum. If not do you have any idea what could be going wrong. Some details of the mdp file: 1. pbc is turned off. 2. there is no pressure coupling. 3. center of mass removal is set to angular. 4. temperature is 298 K and berendsen thermostat is used. 5. energy groups and table are defined (correctly). 6. the cut-offs are set to 1.0nm (box size is larger than 4 nm). 7. no constraints are being used. Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Using user-tables for simulations in vacuum
Hello users, I am trying to do a simulation of a polymer chain (which is simply a bead of unified methane molecules) in vacuum using user-defined tables. The interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However, when I run the simulations, mdrun gives me a segmentation fault. When I run simulations for the exact same configurations without the tables (and therefore using VdW) the simulations run fine. In addition, the starting configurations were obtained after 3ns simulations of the polymer in water. So I was wondering if there is any issue with using user-defined tables with simulations in vacuum. If not do you have any idea what could be going wrong. Some details of the mdp file: 1. pbc is turned off. 2. there is no pressure coupling. 3. center of mass removal is set to angular. 4. temperature is 298 K and berendsen thermostat is used. 5. energy groups and table are defined (correctly). 6. the cut-offs are set to 1.0nm (box size is larger than 4 nm). 7. no constraints are being used. Thank you Regards Sapna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re:Re:[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Hello, Thanks for your response. I have used the same tpr files for both the simulations. I compiled the tpr file in gromacs 3.2.1 and then used that tpr file to run simulations using the two versions of gromacs (i.e. only the mdrun was from different versions). I am not using any dispersion correction. There is also no switch or shift being used. I have pasted the run.mdp file below. The energies are different in the two cases. The LJ(SR) and the Coulomb are both different, resulting in different potential energies (PE) for the two. The PE of gromacs v3.3.1 is higher than that obtained by gromacs v3.2.1 (i.e v3.2.1 is more negative). In the pressure virials, I find that the diagonal terms are the same for the two versions (Vir-XX,YY and ZZ) however the off-diagonal are significantly different (magnitude of v3.2.1 > v3.3.1),given below. Does this information give any indication as to what may be wrong? If not I will submit the tpr file to bugzilla. Thank you Sapna quantity gromacs v3.2.1 gromacs v3.3.1 Pressure (bar)0.5960180.838094 Vir-XX26640.5 26661.2 Vir-XY 6865.12 1.36518 Vir-XZ 6865.210.0121227 Vir-YX 6865.8 1.48257 Vir-YY 26652.3 26642.1 Vir-YZ 6886.45 3.93327 Vir-ZX 6861.23 -0.0529923 Vir-ZY 6882.24 3.87739 Vir-ZZ 2666526647.2 Run.mdp file: title = Water simulation ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step (ps) nsteps = 100 ; number of steps nstcomm = 1; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 100 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw= 1.0 ; cut-off for vdw rcoulomb = 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t= 0.5 ref_t = 300 Pcoupl = Berendsen Pcoupltype= isotropic; pressure geometry tau_p= 0.5 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; reference pressure gen_vel = yes ; generate initial velocities gen_temp = 300 ; initial temperature gen_seed = 2432384243 ; random seed Date: Tue, 18 Dec 2007 08:28:52 -0500 > From: "sapna sarupria" <[EMAIL PROTECTED]> > Subject: [gmx-users] Different system volumes from gromacs versions >3.2.1 and 3.3.1 > To: gmx-users@gromacs.org > Message-ID: ><[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Dear users, > > I had posted this question earlier too but did not get any response. I > am > re-posting it hoping someone can clarify this for me. > > I performed NPT simulations of few different systems using both gromacs > v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, > topology files etc for both the versions. The systems are pure water > system > (spc/e 10684 water molecules) and a protein-water system. However, the > average volume of the system that I get is from the simulations is > different > for the two versions. In case of pure water, gromacs v3.2.1 gives me a > lower > volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is > significantly higher than the fluctuations in the volume. The pressure is > maintained at 1 bar and the temperature is maintained at 300 K using > Berendsen barostat and thermostat respectively. I used SETTLE to maintain > water geometry. I was wondering if someone could tell me why this happens? > Has there been a modification in the pressure virial calculation or > something related to the same that leads to these differences? > > Thank you > > > Regards > Sapna > > -- > Sapna Sarupria > Ph.D. Student - Chemical Engineering > Rensselaer Polytechnic Institute > Troy, New York 12180 > U.S.A. > Ph#: (518)276-3031 > Life isn't about finding yourself. Life is about creating yourself. > George B
[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Dear users, I had posted this question earlier too but did not get any response. I am re-posting it hoping someone can clarify this for me. I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (spc/e 10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I used SETTLE to maintain water geometry. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Dear users, I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
