Justin, Thank you for the guidance.
"You simply supply whatever the LJ combination should be for the 1-4 pair. If you want 0.5 times what is listed, change the values." But this would change the LJ interaction for 1-4 pairs and all other pairs that are not excluded, correct? Consider a UA model of cyclooctane. This has 1 atomtype. If you specify LJ parameters for the CH2 group in the atomtypes directive, GROMACS will apply the unscaled LJ interactions for non-excluded pairs and the scaled LJ interactions for 1-4 pairs. Say you want to implement the same behavior with a nonbond_params directive. Since the directive takes atomtypes, there is no way to specify and scale the 1-4 CH2-CH2 LJ interactions. Am I missing something? Best, Eric On 7/28/18 7:19 PM, Eric Smoll wrote: > On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > >> On 7/26/18 5:52 PM, Eric Smoll wrote: >> >> Hello GROMACS users, >>> >>> I have a quick question about the nonbond_params directive. >>> >>> If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive, >>> GROMACS will >>> >>> That's fudgeLJ, not fudgeQQ, but yes. >> >> (1) compute VDW parameters for all atomtype-pairs and >> >>> (2) scale all 1-4 interactions specified in the pairs directive by 0.5. >>> Note that the parameters for the 1-4 interactions are obtained from (1). >>> >>> Correct. >> >> >> Will GROMACS still scale all 1-4 interactions by 0.5 if I specify VDW >>> parameters for all atomtype-pairs in a nonbond_params directive? >>> >>> No. [nonbond_params] takes precedence. For any missing pair, and with >> gen-pairs = yes, fudgeLJ is used. It is not used for anything else. >> >> > Thanks for the reply. That is dissapointing. Then how does one implement > scaled 1-4 interactions with the nonbond_params directive? It seems > You simply supply whatever the LJ combination should be for the 1-4 pair. If you want 0.5 times what is listed, change the values. On Sat, Jul 28, 2018 at 6:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/28/18 7:19 PM, Eric Smoll wrote: > >> On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 7/26/18 5:52 PM, Eric Smoll wrote: >>> >>> Hello GROMACS users, >>>> >>>> I have a quick question about the nonbond_params directive. >>>> >>>> If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive, >>>> GROMACS will >>>> >>>> That's fudgeLJ, not fudgeQQ, but yes. >>> >>> (1) compute VDW parameters for all atomtype-pairs and >>> >>>> (2) scale all 1-4 interactions specified in the pairs directive by 0.5. >>>> Note that the parameters for the 1-4 interactions are obtained from (1). >>>> >>>> Correct. >>> >>> >>> Will GROMACS still scale all 1-4 interactions by 0.5 if I specify VDW >>>> parameters for all atomtype-pairs in a nonbond_params directive? >>>> >>>> No. [nonbond_params] takes precedence. For any missing pair, and with >>> gen-pairs = yes, fudgeLJ is used. It is not used for anything else. >>> >>> >> Thanks for the reply. That is dissapointing. Then how does one implement >> scaled 1-4 interactions with the nonbond_params directive? It seems >> > > You simply supply whatever the LJ combination should be for the 1-4 pair. > If you want 0.5 times what is listed, change the values. > > impossible since this directive accepts atom types, not atom numbers. >> > > In what instance do you want the same LJ pair to have different > interactions? That would be a recipe for a totally non-transferable force > field. > > -Justin > > > >> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> ================================================== >>> >>> -- >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.
