Hi Berk, Thanks for your answer, I am happy to have the priority list for how the van der Waals term of the pair potential is calculated.
About fudgeQQ, do you mean that the pair potentials' coulomb terms are scaled with the fudgeQQ value, even when "gen-pairs" is set to "no"? ( I see from the manual that "FudgeLJ is only used when generate pairs is set to 'yes', so maybe your answer is already given in the manual. Actually, I am not sure if this statement is an implicit information about FudgeQQ..) -Soren From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Berk Hess Sent: Thursday, July 30, 2009 4:33 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] generate pair list and 1-4 interactions Hi, The charges are always scaled with fudgeQQ. For the LJ parameters the precendence is: For an atom pair in the [ pairs ] section with type A and B: if parameters are present on the line in the [ pairs ] section use those, otherwise if parameters are present in the [ pairtypes ] section use those, otherwise if gen-pairs=no generate a fatal error, otherwise if parameters for A-B are present in the [ nonbond_params ] section scale with fudgeLJ and use those, otherwise use the parameters for A and B in the [ atoms ] section and scale with fudgeLJ and use those. Berk ________________________________ Date: Thu, 30 Jul 2009 15:58:40 +0800 From: ch...@nus.edu.sg To: gmx-users@gromacs.org Subject: [gmx-users] generate pair list and 1-4 interactions Dear all, I am a bit confused about how the pair potentials (PPs)are calculated. If I state explicitly sigma and epsilon values for the pair potentials, can I then still have a coulomb scaling of my 1-4 interactions? Say I set "gen-pairs" to "yes", although I have all possible pair potential interactions specified under "[ pairtypes ]", would I then still be able to scale my 1-4 coulomb interactions by setting a "FudgeQQ" different from 1? Also, would I be able to scale the already given van der Waals interactions with "FudgeLJ"? Finally, are generated pair potentials based on the parameters specified under "[ atomtypes ]" or "[ nonbond_params ]" (if the latter exist) in the ffamber03nb.itp file? Best regards, Soren Enemark ________________________________ Express yourself instantly with MSN Messenger! MSN Messenger <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
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