Hi Mark, Thanks for your reply! I'm sorry, you're right, as far as I know the manual doesn't actually mention Buckingham pairs generation... but when I set gen-pairs to "yes" and run grompp, I get the following error:
"Generating pair parameters is only supported with LJ non-bonded interactions" I guess I'm wondering how anyone can use the Buckingham potential at all, since Gromacs does not appear to support pairs generation for the Buckingham or the use of explicitly defined Buckingham pair parameters (when defining [ pairtypes ], you have to give the parameters in LJ form). Thanks so much again, Olivia On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham <[email protected]>wrote: > > > On 29/12/11, *Olivia Waring *<[email protected]> wrote: > > I apologize for the truncated message; I pressed send too soon. > > According to the Gromacs manual, pairs cannot be generated automatically > for the Buckingham potential, > > > Where does it say this? > > > but the [ pairtypes ] directive seems to only accept parameters in LJ form > (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to > interconvert between the two potential forms, but haven't found anything... > Can anyone who has successfully generated a topology using the Buckingham > potential shed light on this issue? > > > You want a 1-4 interaction using Buckingham functional form? If so, I > don't think GROMACS supports it. If you're trying to combine bits of force > fields that use L-J with bits of force fields that use Buckingham, then > that's almost certainly a bad idea. > > Mark > > > > > Thank you so much, > Olivia > > On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring <[email protected]>wrote: > >> Hello Gromacs users, >> >> I'm using a Buckingham potential for the nonbonded interactions in my >> system, so I have the following lines in my forcefield.itp file: >> >> [ defaults ] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> 2 1 no 1.0 1.0 >> >> >> >> >> -- >> Olivia Waring (王维娅) >> Princeton University '12 >> AB Chemistry >> >> > > > -- > Olivia Waring (王维娅) > Princeton University '12 > AB Chemistry > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
