Re: [gmx-users] Why density increase with increasing the cutoff length?
On 12/21/09 8:55 AM, XAvier Periole wrote: Would it be all cut-offs: elect + vdW ? Or the increase is separate? For your info the vdW are attractive potentials at long distances so an increase of cutoff would result in an increase of attraction and therefore to an increase of density! This is one good illustration of the fact that you should not change the cutoff values from the ones used for the parameterization of a force field. In general I agree, however for some popular force fields like OPLS this is not so well-defined. Jorgensen uses different cut-offs in different papers. Using PME and dispersion correction means you are almost independent of the cut-off length (if they are not too short). Typically 1 nm and upwards will give you the same results with these settings. If you're using plain cut-offs or RF you're on your own. On Dec 21, 2009, at 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing list 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. 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. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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] Why density increase with increasing the cutoff length?
From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. Arden Perkins On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song yson...@asu.edu wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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
Re: [gmx-users] Why density increase with increasing the cutoff length?
From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. This point of view implies that the potentials used are perfect and then indeed the longer cutoff you use the more accurate your interactions energies become. You have to consider that current potential are parameterized to reproduce some data (structural and thermodynamics experimental data) and this using a given cutoff. Modifying the cutoff means that you modify the potential and therefore the model will not necessarily (and most often) fit the experimental data anymore. Arden Perkins On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song yson...@asu.edu wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 -- 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] Why density increase with increasing the cutoff length?
Arden Perkins wrote: From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. A higher cut-off does not necessarily indicate higher accuracy, for the parameterization process used a particular cut-off. The model physics is defined by all of the functional form, parameters, cut-offs, etc. The validity of the parameters is intrinsically linked to that cut-off. One might be able to demonstrate that one can get equivalently valid results with a different (i.e. longer) cut-off, but then there's not yet a demonstrated *increase* in accuracy. If the same parameters can produce a better model physics at a longer cut-off, then there's probably a case for further parameterization to do equivalently well for lower cost. All this assumes a non-Ewald method. PME is a different matter entirely. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. A higher density for a given cut-off increases the number of interaction partners for each atom, but that implies nothing about the accuracy of the model of that system at that density. A move from one density to another during equilibration at a given cut-off tends to indicate the unsuitability of the model physics at the former density. Xavier Periole: But I think we all agree on these issues: the treatment of long-range interactions are delicate :)) Agreed, treating long-range interactions is delicate :-) Mark On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song yson...@asu.edu mailto:yson...@asu.edu wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 -- 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] Why density increase with increasing the cutoff length?
Thanks for all the helpful response. But do I have to use dispersion correction when I use PME? I don't quite understand what dispersion correction do. Sometime I found using dispersion correction make my results worse for a large molecule system. On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 12/21/09 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University Van der Waals interactions. I guess you have not turned on the dispersion correction. If you do the effect should be far less. -- 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. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] Why density increase with increasing the cutoff length?
On 12/21/09 5:32 PM, Yanmei Song wrote: Thanks for all the helpful response. But do I have to use dispersion correction when I use PME? I don't quite understand what dispersion correction do. Sometime I found using dispersion correction make my results worse for a large molecule system. Read the manual please. On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 12/21/09 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University Van der Waals interactions. I guess you have not turned on the dispersion correction. If you do the effect should be far less. -- 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. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- 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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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] Why density increase with increasing the cutoff length?
On 12/21/09 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University Van der Waals interactions. I guess you have not turned on the dispersion correction. If you do the effect should be far less. -- 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. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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] Why density increase with increasing the cutoff length?
Would it be all cut-offs: elect + vdW ? Or the increase is separate? For your info the vdW are attractive potentials at long distances so an increase of cutoff would result in an increase of attraction and therefore to an increase of density! This is one good illustration of the fact that you should not change the cutoff values from the ones used for the parameterization of a force field. On Dec 21, 2009, at 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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
