Exactly a factor of ten? Angstrom vs nm issue?
On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy <are...@csir.co.za> wrote: > Greetings, > > I am trying to use tabulated potentials for the VdW interactions between > TIP5P water molecules. > I have tested my topology file to make sure that it gives reasonable > results > with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , > C12=4*eps*sig^12. I am able to match the energies with an identical run > not > using look-up tables. The problem comes when I want to include the C6 & C12 > parameters within the table. This is needed for dealing with more complex > multi-parameter potential functions. > > I tried testing this with the standard Lennard-Jones potential. Setting > g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my > table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)] > > I set vdw-type = user in my mdp file and modified my topology so that: > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 0.5 0.8333 > > [ atomtypes ] > ; name at.num mass charge ptype C6 C12 > OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00 > > Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg > and C6=4*eps*sig^6 , C12=4*eps*sig^12 > The run proceeds fine with no warnings or errors, but the LJ and Potential > energies are an order of magnitude higher than when using the standard > table. I don't understand why I am not able to reproduce the results by > this > method? > > Thanks, > Andrish > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
