[gmx-users] free energy problem

gives many lincs warnings when it is turned on, and lambda = 0 to 0.5. Ultimately, the run crashes. One thing that I can think of that may be a problem is that state B has a nonzero charge, while A is 0. I have attached my run input, and topology. Any help is very much appreciated. Thanks.  Elio Cino

[gmx-users] Free energy problem

Hi Berk. Thanks for the response. If I am looking to find the free energy of binding of the peptide to the globular protein, then I do not know how else to approach the problem besides using my "brute-force" approach. Do you have any alternative ideas?

[gmx-users] free energy cycle and couple-intramol setting

vacuum simulation required here? If so, any guidance on the appropriate settings would be appreciated. Thanks.  Elio Cino ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] standard state correction of delta G from a PMF

some papers that do standard state correction. So if anyone has the time to explain this again in a more basic manner it would be appreciated. Thanks.  Elio Cino -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] standard state correction of delta G from a PMF

ar on what is going on.  Elio Cino -- 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

[gmx-users] standard state correction of delta G from a PMF

or by integrating different areas. I have been using the region up until the plateau as bound and the plateau region as unbound. Thanks. Elio Cino -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

[gmx-users] new beta release - gromacs-4.5-beta2

testing. Thanks for the new release. Elio Cino -- 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

[gmx-users] new beta release - gromacs-4.5-beta2

  userint1                 = 0 userint2                 = 0 userint3                 = 0 userint4                 = 0 userreal1                = 0 userreal2                = 0 userreal3                = 0 userreal4                = 0 Elio Cino -- gmx-users mailing listgmx-users@gromac

[gmx-users] new beta release - gromacs-4.5-beta2

linux machine runs fine. Elio Cino -- 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

[gmx-users] gromacs-4.5-beta2 implicit solvent lincs errors

the latest git with the same results.  Elio Cino -- 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