You were right, it's much faster when I only calculate free energy for one molecule. My simulation has 1000 water molecules in it, but I created a new topology file and gave one molecule a different name (but identical properties) and now it runs the same simulation in about 36% more time, which is much more manageable. Thank you very much for the help! I don't think there is a problem with my topology or mdp files now.
Regards, Nathan H. ----- Original Message ----- From: "Michael Shirts" <mrshi...@gmail.com> To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> Sent: Wednesday, October 7, 2015 11:14:29 PM Subject: Re: [gmx-users] Free Energy of Liquid Water If ALL the particles are changing with the free energy coupling parameter, then GROMACS will slow down quite a bit. If only one molecule is changing, then it shouldn't be that much slower (20-30% slower?) But without .mdp and.top files, it's hard to say exactly what is happening. On Wed, Oct 7, 2015 at 11:08 PM, Nathan K Houtz <nho...@purdue.edu> wrote: > Thanks for explaining, (and Professor Farais de Moura as well) that makes > sense. > > On a different note, I've noticed a huge difference in performance between my > equillibration run and my actual simulation, and I'm wondering if this is > normal. For comparison, I ran a couple small (meaningless) simulations where > the only difference was the collection of free energy information and Gromacs > slows down by a factor of 39. I had been under the impression that I would be > able to do each simulation in just under an hour but now it looks like it > will take the better part of two days, which is too much. I'll just have to > run shorter or fewer simulations if I can't improve that, but I'm hoping I'm > just doing something wrong. I'm essentially using modified versions of the > .mdp file I found for this tutorial: > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy. > I changed things like turning off the pressure coupling, changing the > temperature, etc. The settings for free energy calculations are unchanged. Is > the calculation of dh/dl re > ally that expensive, or is this abnormal? > > Thank you for the help as always. Regards, > Nathan H. > > ----- Original Message ----- > From: "Michael Shirts" <mrshi...@gmail.com> > To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> > Cc: "gromacs org gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> > Sent: Tuesday, October 6, 2015 3:05:38 PM > Subject: Re: [gmx-users] Free Energy of Liquid Water > > For a pure fluid, G = N \mu. And \mu = (dG/dN)_(T,P). So you only > need to change one molecule to ideal gas to get the change in free > energy. The free energy of transfer of water from liquid to gas is > indeed the free energy of solvation of one water molecule in bath of > water. So there's a reason why you're just finding tutorials of > solvation free energies! > > On Thu, Oct 1, 2015 at 10:44 PM, Nathan K Houtz <nho...@purdue.edu> wrote: >> Hi everyone, >> >> I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid >> water (TIP4P model) to an ideal gas, to find the relative free energy. To do >> this, I believe one generally integrates above the critical point by >> increasing the temperature above the critical temperature and then relaxing >> the pressure until the system is a diffuse gas. The mdp options >> documentation is helpful, and I went through an ethanol solvation tutorial, >> but there doesn't appear to be a "pressure-lambda" or a "volume-lambda" >> option that I could use to do the second part. How can I get Gromacs to >> calculate the dh/dl derivative while relaxing the pressure? >> >> In addition, all of the tutorials I found for thermodynamic integration were >> for finding solvation free energies. The coulomb and VDW forces are >> essentially changed from "completely on" to "completely off". But in my >> case, I'd like to change the temperature and pressure between two nonzero >> values. I don't want to begin my simulation at 0K and 0atm, but lambda >> *must* go from 0 to 1. How can I define both starting and ending points for >> the temperature and pressure (or volume, or density)? >> >> Thanks for your help! >> Nathan H. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- 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.
