Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful.
I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it? I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum. Thank you, Bhagyesh ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Thursday, June 29, 2017 6:48:25 PM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > I am getting the same following warning even after minimizing the system > twice using cg integrator. This is only when the free energy stuff is > inserted in the energy minimization code. > > " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at > distance 3f which is larger than the table limit 3f nm. > > This is likely either a 1,4 interaction, or a listed interaction inside a > smaller molecule you are decoupling during a free energy calculation. Since > interactions at distances beyond the table cannot be computed, they are > skipped until they are inside the table limit again. You will only see this > message once, even if it occurs for several interactions. > > IMPORTANT: This should not happen in a stable simulation, so there is > probably something wrong with your system. Only change the table-extension > distance in the mdp file if you are really sure that is the reason. " > > > When the system is minimized without free energy code, it shows no warning. > Hence, I suppose it is due to the free energy code itself with > couple-intramol = no. > > I found the warning disappears when couple-intramol = yes. But this is not I > would like to do, since intra molecular interactions need not be > scaled/perturbed. > > It's definitely true that the "listed interaction inside a smaller molecule > you are decoupling during a free energy calculation". > > When the table-extension is increased to 4 nm with couple-intramol = no, the > warning again disappears. Should I go forward with this setting and how will > it affect the energy minimization of my system? > Increasing the table-extension means mdrun will permit distorted structures that may be totally unreasonable. It is generally unwise to increase it, and especially if you're increasing it that much. -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.
