On Thu, Jul 16, 2015 at 1:24 PM Ming Tang <m21.t...@qut.edu.au> wrote:
> Dear Justin, > > Thanks. > 1. The total Lennar-Jones 12-6 energy of the whole system is the addition > of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition > of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your > explanation right? Besides, in Gromacs, is the potential energy the > addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, > LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR? > You are right. That's why I don't get the LJ-LR and Coulomb-LR options > when using g_energy. Suddenly, I realised that my understanding of the > twin-range approach was totally wrong. For cutoff-scheme = verlet, rlist > cannot be smaller than rvdw = rcoulomb, and When using twin-range method, > either coulombtype = cut-off with > rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean > that for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme = > verlet? However, even if I set vdw-modifier = potential- switch, the > rlistlong larger than rlist is reset to be equal to rlist by gromacs, and > there is not LJ-SR option when using g_energy. I am totally lost. Can you > help to tell me how does twin-range work when cutoff-scheme = verlet? > http://manual.gromacs.org/documentation/5.1-rc1/user-guide/cutoff-schemes.html (and equivalent docs for earlier versions) indicate that twin-range is not supported by the Verlet scheme. (Technically, it could be supported, and some forms of it are in fact used by the PME-tuning facility, but some of us are unconvinced of the technical merit of such forms, nor do we like the confusion created by how such group-scheme features are named and implemented in GROMACS. So, if there is ever support, it's likely to be from a clean slate, and after we remove the group scheme.) Another question is I used the following code to make my cut-off parameters > be consistent with those used for the triple-range cut-off scheme in the > paper defining Gromos 54a7 force field: > > coulombtype = reaction-field > coulomb-modifier = potential-shift > rcoulomb-switch = 0.8 > rcoulomb = 1.4 > epsilon_rf = 61 > > Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable. > But rlist should not be smaller than rcoulomb when cutoff-scheme = verlet. > How to achieve this triple-range cut-off scheme? > You can't. Mark > 2. The pull rate I use is 4e-5/ps. I thought it is small so that the > energy of water can be treated as constant during the pull process. I > forgot to consider the water-protein interaction and that my pull rate is > much larger than the pull rates used in the experiments which is in order > of micrometre per second and is much more relevant to physiological pulling > rate. You are right, I cannot treat the trends of the system's energy as > those of the protein's energy. But how can I get the energy of the protein? > Is it feasible to set all the atoms of the protein as one energy group, and > do rerun to achieve this? > > Thanks, > Regards > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin > Lemkul > Sent: Thursday, 16 July 2015 11:20 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] LJ-14 energy > > > > On 7/15/15 8:39 PM, Ming Tang wrote: > > Dear Chaban and Justin, > > > > > > > > Sorry for the mis-action. Please ignore my last email. > > > > > > > > Thank you both for your free help. > > > > I am pulling a collagen triple helix in a periodic water box using > > umbrella direction-periodic. I want to calculate the Lennard-Jones > > 12-6 of the protein. According to Gromacs manual, it contains > > repulsive short-range term and attractive long-range term. Is the > > Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am > > interested in the energy trends more than > > LJ-LR only exists with a twin-range cutoff approach. The total LJ between > any groups also includes LJ-14 for intramolecular terms. Intermolecular LJ > would be the sum of LJ-SR and LJ-LR, if the latter exists. > > > the energy absolute values. So, if I can calculate the LJ 12-6 of the > > whole system, it is fine, because I can assume the energy of the water > > is not subject to change due to pulling. > > > > Why can you assume that? You're pulling a structure, which is a > non-equilibrium process. There will be different interactions as a > function of time. > Water-water interactions at long distance from the protein indeed are > unlikely to be affected, but those close to the protein may be different > (though electrostatics/hydrogen bonding are probably much more interesting). > Water-protein interactions certainly can't be assumed to be unchanging > during pulling. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.