>From my own reading the Berger values are already scaled so to include them in gromacs by themselves no scaling would be required (like fudge=1.0). However OPLS 1-4 should be scaled by 0.5. So Chris Neale's method is to use fudge = 0.5 for OPLS and include the berger values twice. Here is a summary of what helped me understand the method from Chris Neale's posts:
"As the lipid.itp already has defined a pairtypes so that LJ 1-4 is scaled correctly (fudgeLJ is not applied to the values in [pairtypes] if there is a [ pairs ] section ) but the lipid fudgeQQ will be set to 0.5 instead of 1. If we divide the epsilon entries in the [ pairtypes ] of the lipid by two now both the LJ and coulombic 1-4 are exactly half of what they should be." "Then include each entry in [pairs] twice so now LJ and coulombic 1-4 are both at what they should be." This is a little confusing as you have to half the LJ value so you can double it later along with the Q. Again: "The pairs section defines both the Lj and the Q so we will have double of each. We only want double Q, since it is cut to half by the OPLS fudgeQQ value but not double epsilon(LJ) as it already has a special pairtypes section which is properly modified for 1-4 interactions." More info: defining [pairtypes] automatically switches off the fudgeLJ option. Hope this helps, Oliver 2011/2/25 <mirc...@sjtu.edu.cn> > Dear All: > > I am using GROMACS package to simulate membrane proteins. I plan to use > Berger's united atom force field (Berger's UA FF) for lipids and OPLS_AA > force field (OPLS_AA FF) for proteins. > > I have read the guide post kindly by Prof. Dr. Chris Neale in previous > mailing lists very carefully. According to his guide, the following steps > are needed: > > 1). Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after changing > c6/c12 > to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected > by > pope.itp > - sigma = (c12/c6)^1/6 > - epsilon = c6/(4*sigma^6) > > 2). Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing > c6/c12 > to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all > reference > to OW to opls_116 (opls spc water oxygen) and simply removed any with > reference > to HW as it will be zero regardless. > > 3). Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp. > - Prior to running ensure that the non-RB dihedral does not exist for > these > groups. > > 4). make a topology file like this: > > My questions are as follows: > > 1, Berger's United atom force field scale LJ1-4 interaction by 0.125 and > scale Coulombic1-4 interaction by 1.0. OPLS_AA FF scale both of them by 0.5, > right? From the above changes, I find that the changes of the sigma or > epsilon (or c6 and c12) is only associate with the LJ1-4 interaction. So, > how the Coulombic1-4 interaction is scaled properly? Do I need additional > changes? > > 2, the non-bond interactions between the atoms from the lipid and the atoms > from the protein are need to be calculated, right? My question is how these > interactions are calculated? Does the changes in the [atomtypes]affect these > interactions? > > 3, How the non-bond interactions between the atoms from the lipid are > calculated (e.g., the LJ and coulombic interactions)? Does the changes in > the [atomtypes]affect these interactions? > > Thank you very much for your time and your kindness. I really appreciate > your help. > > Regards > > Ruo-Xu Gu > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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