Gavin Melaugh wrote:
Hi Justin
Thanks for replying. I have checked the energy file and there are no 1,4
terms, which is what I expected. I should clarify that my parameters are
taken from the OPLS ua forcefield but I have relabelled them for my own
model, which is not a common molecule. Therefore all the info on the
molecule is in .top and obviously the .gro file. i.e. there are no
#include statements. Now I take it that the non-bonded LJ are taken from
the [atom types] directive? The question is then how and where do I
state the 1,4 terms. I always thought that when gen-pairs = yes, then
gromacs would generate a list of all the 1,4 interaction types?
You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a
[pairtypes] directive, you do need a [pairs] directive to dictate the 1-4
interactions. Setting "gen-pairs = yes" generates the parameters, such that a
[pairtypes] directive is unnecessary.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi all
Can someone please get back to me on this. I have generated my own
topology file from OPLS parameters by hand with the following format. I
am now concerned that I haven't been calculating 1,4 interactions, which
I thought were generated by setting gen-pairs = yes. I have read section
5 of the manual several times but am still unclear about this.
You can answer this question by analyzing your .edr file: are there
LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4
interactions. Seems to me that, for OPLS, your approach is fine. It
wasn't clear from your earlier posts that you were using OPLS, hence
the inability to know if what you were doing was right or not.
Different force fields have different underlying mechanics, so the use
of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent
upon your model.
-Justin
Cheers
Gavin
parameter level
[defaults]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
[atomtypes]
;type mass charge ptype sigma(nm)
epsilon(kjmol-1)
;Molecular level
[moleculetype]
; name nrexcl
tertpentane 3
[atoms]
; atomnr type resnr residue name cgnr charge mass
[bonds]
; ai aj func b0(nm) kb(kjmol-1 nm-2)
[angles]
; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2)
[dihedrals]
;System level
[system]
[molecules]
; moleculename number
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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