[gmx-users] RB dihedral potential query in OPLS
alokjain at iitk.ac.in
alokjain at iitk.ac.in
Tue Sep 12 16:49:30 CEST 2006
hello gmx users,
First of all thanks to Chris for his response to my
previous mail.But I still have a doubt regarding RB
potential which I would like to get clarified about.
I would be very thankfull if you can go through my
post (patiently) and comment on it.
___________________________________________
Gromacs 3.2 manual states " The use of RB potential implies exclusion of
LJ interactions between the first and the last atom of the dihedral..."
I also searched the mailing list and came accross a response from David to
one of the queries which is as follows:
"The original Ryckaert Bellemans potential is for carbon tails only (e.g.
decane, or lipids). The same potential is used in OPLS but with different
parameters in which the(scaled) pair interaction is part of the
parameterization"
http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html
Gromacs 3.3 manual along with the above mentioned statement in manual 3.2
also states that:
"Ryckaert-Bellemans potentials are also used in e.g. the OPLS force field
in combination with 1-4 interactions. You should therefore not modify
topologies generated by pdb2gmx in this case".
------------------------------------------------------------
I presently ran a MD simulaiton of a protein solvated in water using
gromacs 3.2.1 and OPLS-AA force filed.A energy output in the log file
looks like:
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.15231e+03 2.92374e+03 1.73760e+02 1.32334e+03 1.86599e+03
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
5.03326e+03 1.39004e+05 -1.66722e+03 -9.54632e+05 -5.37046e+04
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-8.58528e+05 1.57277e+05 -7.01250e+05 3.04174e+02 -4.80269e+01
So I have a Ryckaert-Bell. energy term for Proper dihedral potential.
I also have a 14 terms for LJ and Coulomd energy.
My initial impression was that once we use the RB dihedral term,we may
actually not get the 14 term in my energy profile (Manual 3.2)
But after going through the manual 3.3 and also Divid's post,I suppose
that the parameters in OPLS-AA are so defined that RB potential along with
the 14 interactions (scaled) are calculated seperately.
Is this the case?????
PS: Chris suggested me to check the [pairs] and [dihedral] entry in the
*.top (*.itp) file which I did and I found identical atoms in both the
entries which according to Chris should not be the case...So I am more
confused.
Regards.
Alok Jain.
>
>>In manual (chapter 4 page no 62) it was written The use of RB potential
>>implies exclusion of LJ interaction between first and the last atom of
>> the
>>dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14
>>energy in my log file (see below) is there is any problem in this
>>simulation or it is normal?
>
> Only the 1-4 interactions spanning RB potentials should be excluded from
> LJ-14
> and coulomb-14. For example, lipid headgroups may be treated without RB's
> and
> the acyl chains treated with RB's. If you want to see where things are
> coming
> from, make an index file and then use enerygrps in your .mdp so that
> g_energy
> can give you some useful output for further testing. Look at your [ pairs
> ]
> section in your .itp file. Those are the source of the LJ-14 and
> Coulomb-14
> energies.
>
>>and what I understood from articles on OPLS force field that it scale
>> down
>>the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in
>>ffoplsaa.itp file
>>what about GROMOS96 force field, it is mention in manual (Chapter 4 page
>>no 75) it also scale down the LJ-14 repulsion term .
>>what I understood by manual that It uses separate parameter for LJ-14
>>interaction Is it is correct? If yes then It uses separate parameters
>> only
>>for LJ repulsive term or all the non bonded terms i.e. LJ repulsive,LJ
>>attractive and for coulomb term?
>
> The .itp file for your molecules will have the information that you are
> after.
> 1. The [ pairs ] section is a list that defines what 1-4 interactions
> exist. If
> a 1-4 pair is not in the [ pairs ] section, LJ-14 and Coulomb-14
> interactions
> will not be included in the energies.
>
> **That's a good test for you right there. Remove all entries from the [
> pairs ]
> section and your 1-4 energies should drop to zero.
>
> 2. The charges for 1-4 interactions are the normal ones, and FudgeQQ will
> be
> applied.
> 3. The LJ sigma / epsilon parameters will be taken from [ pairs ] if they
> are
> there, or (second in hiearchy) from [ pairtypes ] if they are there, or
> (third
> in hiearchy) generated from the regular non-bonded parameters if
> gen-pairs=yes.
> In this third case, FudgeLJ is applied.
>
> Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but
> these
> apply to the information outlined above. For example, gen-pairs does NOT
> mean
> "generate a [ pairs ] section for the molecule." Instead, it means "If
> LJ-14
> epsilon and sigma are not present in a [ pairs ] section entry, and that
> type of
> interaction is not explicitly formulated in [ pairtypes ], then it is
> permissible to use the regular non-bonded parameters, and in that case
> scale
> them by FudgeLJ."
>
> OPLS-AA uses gen-pairs=yes, Force-fields that use gen-pairs=no (GROMOS96 I
> think) will have a very large [ pairtypes ] section. FudgeLJ is not used
> when
> gen-pairs=no, but FudgeQQ is always used. Note that it is perfectly
> reasonable
> to scale the 1-4 FudgeQQ/LJ and set gen-pairs=no.
>
> If there is still misunderstanding, do a search for {pairs pairtypes}.
>
> Also, if your main concern is ensuring that you don't have any 1-4
> interactions
> where you shouldn't then I would recommend drawing out your molecule and
> making
> sure that you don't have any RB dihedrals defined with an overlapping
> entry in
> the [ pairs ] section. However, this is not absolutely going to work
> because it
> gets complicated sometimes. Eg: I have yet to figure out exactly why
> things are
> treated as they are in the [ pairs ] section for two non-RB double-bonded
> carbons in the middle of a long chain of RB carbons :: more specifically I
> am
> referring to lipid acyl chains with a double bond (for example pope.itp
> from Dr.
> Tieleman).
>
> Chris.
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