Re: Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables
lloyd riggs wrote > > > Dear Andrish Reddy, > > > > Dont know if it works but I have for small molecules just put all the > parmeters within the .top file right below the defaults, instead of user > defined tables, and removed the "forcefieldX/SPC.itp" or > equivalent section so it doesn't loop, but dont know if it works in > your case. Just a quick suggestion to try, as I parse e-mails. > Smone else probably has better answeres though... > > > > Stephan > > > Gesendet: Mittwoch, 22. Mai 2013 um 16:09 Uhr > Von: "Andrish Reddy" < > areddy@.co > > > An: > gmx-users@ > > Betreff: [gmx-users] C6 & C12 parameters for non-bonded > interactions using tables > > 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. A 1.0e+00 1.0e+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@ > > 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-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > gmx-users mailing list > gmx-users@ > 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-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Thanks Stephan, Don't think that will work in my case. Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449p5008456.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables
Dear Andrish Reddy, Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the "forcefieldX/SPC.itp" or equivalent section so it doesn't loop, but dont know if it works in your case. Just a quick suggestion to try, as I parse e-mails. Smone else probably has better answeres though... Stephan Gesendet: Mittwoch, 22. Mai 2013 um 16:09 Uhr Von: "Andrish Reddy" An: gmx-users@gromacs.org Betreff: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables 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. A 1.0e+00 1.0e+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 listgmx-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
Re: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables
Exactly a factor of ten? Angstrom vs nm issue? On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy 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 ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 0.5 0.8333 > > [ atomtypes ] > ; name at.num mass charge ptype C6 C12 > OW_tip5p 8 16.000. A 1.0e+00 1.0e+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 listgmx-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 listgmx-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] C6 & C12 parameters for non-bonded interactions using tables
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 ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype C6 C12 OW_tip5p 8 16.000. A 1.0e+00 1.0e+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 listgmx-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
