[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein
olivercgrant at gmail.com
Tue Mar 1 14:21:02 CET 2011
>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.
"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."
automatically switches off the fudgeLJ option.
Hope this helps,
2011/2/25 <mircial at 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
> to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected
> - sigma = (c12/c6)^1/6
> - epsilon = c6/(4*sigma^6)
> 2). Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing
> to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all
> to OW to opls_116 (opls spc water oxygen) and simply removed any with
> 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
> 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
> 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
> 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.
> Ruo-Xu Gu
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