[gmx-users] Realistic water simulation
Dear All, Is it realistic to perform simulations of a SPC water system consisting on 864 elements. Should I increase the size? The force field used is OPLS-AA/L. Thank you very much. Best, Mario -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force
Dear gromacs users, I would like ask a question about the force of umbrella sampling. I did umbrella sampling by pulling a water molecule from gas phase to organic coated bulk water. I estimated the free energy profile on this reaction coordinate. In order to calculate the random force-force auto-correlation I need to extract the random force on pulled molecule. The force along a reaction coordinate consists of three terms, (i) the mean force as the derivative of the free energy surface, (ii) friction, and (iii) random force. I used gromacs tool g_traj to extract the force on pulled molecule however I do not know how to get the random (iii) force out of it. I would greatly appreciate it if you kindly give me an advise about a way to extract random forces from the overall forces? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hamiltonian REMD
Could you please tell me how I can perform Hamiltonian replica exchange simulations in Gromacs version 5.0.4 without using PLUMED? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hamiltonian REMD
Most of this should still be applicable for 5.0.4. http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy On Wed, Nov 25, 2015 at 6:23 AM, Sanja Zivanovic wrote: > Could you please tell me how I can perform Hamiltonian replica exchange > simulations in Gromacs version 5.0.4 without using PLUMED? > > Thanks > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Realistic water simulation
On 25/11/15 13:02, Mario Fernández Pendás wrote: Dear All, Is it realistic to perform simulations of a SPC water system consisting on 864 elements. Should I increase the size? The force field used is OPLS-AA/L. quite realistic but far from perfect. Read the literature! I assume you mean TIP4P or TIP3P. TIP4P, in particular in one of the later incarnations /Ew or /2005 is probably superior and still cheap. Thank you very much. Best, Mario -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Realistic water simulation
Dear David, Thank you very much for your answer. I am using a flexible version of the model from http://journals.aps.org/prb/abstract/10.1103/PhysRevB.31.2643 Cheers, Mario 2015-11-25 16:16 GMT+01:00 David van der Spoel : > On 25/11/15 13:02, Mario Fernández Pendás wrote: > >> Dear All, >> >> Is it realistic to perform simulations of a SPC water system consisting on >> 864 elements. Should I increase the size? >> The force field used is OPLS-AA/L. >> > quite realistic but far from perfect. Read the literature! > I assume you mean TIP4P or TIP3P. TIP4P, in particular in one of the later > incarnations /Ew or /2005 is probably superior and still cheap. > > >> Thank you very much. >> >> Best, >> Mario >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NPT compress Box using negative Pressure
On Wed, Nov 25, 2015 at 1:49 AM, Christian Bope Domilongo wrote: > > Dear all, > > Need help on how to set negative pressure in order to compress the Box. > I have used negative pressure (-0.2) but the box is still expending. > > ; Pressure coupling > Pcoupl = parrinello-rahman > Pcoupltype = semiisotropic > nstpcouple = -1 > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau-p= 1.0 1.0 > compressibility = 0 4.5e-5 > ref-p= 1.0 -0.2 > > Regards, > Bope Dear Bope, I would expect that *positive* pressures would compress the box. If you set the reference temperature to a negative value, the barostat would tend to increase the box volume such that the pressue measured in the box drops to the negative reference value. Try a positive reference pressure. -0.2 is a really small pressure, much smaller in absolute value than the typical fluctuations in NPT. Is this value sensible? What pressures would you expect experimentally to comprepress your box? How dense is your box? Do you have a dense liquid or a low density gas? Vacuum? Are you trying to compress your box (in the z-direction) so the box height is adequate in order to reproduce some density? In this case you are running a pre-equilibration and maybe the berendsen barostat would give you better results (converge faster, flucutuate less). All depends on what you are trying to accomplish. Greetings from a cloudy yet hot Natal, -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] service broken?
Hello: I am trying to download the latest CHARMM forcefield for Gromacs from: http://mackerell.umaryland.edu/charmm_ff.shtml However, I cannot connect to it in the last 10 days. Does anybody have any idea what's happening? thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
