On 12/10/12 3:13 PM, Andrew DeYoung wrote:
Javier and Mark,
Thank you SO much! That is so helpful to me.
If you have time, I have two follow-up questions:
(1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified
in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are
provided in [ atomtypes ] in ffnonbonded.itp.
But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a
protein for example? I think that in OPLS, such interactions are to be
considered at full strength (no scaling down). My question is: are these
1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions automatically taken
into account if gen-pairs = yes?
Anything beyond a 1-4 interaction is treated as a normal nonbonded interaction
if nrexcl = 3. The [pairs] section has no relevance to these unless you hack
the topology to treat them as such (which you shouldn't).
(2) Suppose that I run grompp (where 1-4 interactions are specified in [
pairs ] and gen-pairs = yes) and grompp gives me the following output:
Generated 276 of the 276 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 276 of the 276 1-4 parameter combinations
Does this output indeed imply that the ONLY nonbonded interactions
considered are 1-4 interactions? In other words, does this output suggest
that NO 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions are
considered? If so, why is this the case if I have set gen-pairs = yes?
That output is only relevant to 1-4 interactions. Since you have gen-pairs =
yes, then anything not listed in a [pairtypes] directive is generated
(calculated) from sigma, epsilon, and the fudge factor relevant to the force
field. Other force fields use [pairtypes] to specify custom interactions for
different combinations of atom types. OPLS-AA is not one of these.
Also, you may find this explanation helpful:
http://lists.gromacs.org/pipermail/gmx-users/2009-July/043326.html
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
