Gavin Melaugh wrote:
A few points then,
1) So a [pairs] directive would include all the atom indices of the 1,4
interactions and the coressponding values of sigma and epsilon?, which I
would do manually.
No. A [pairs] directive simply lists the pairs of atoms for which 1,4
interactions should be calculated. No parameters are listed here. Format:
atom_i atom_j func_type
2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions
which are not present in the pair list from normal LJ parameters using
Fudge LJ". Sorry if I am coming across stupid, but that seems different
to what you're saying?
Not at all. The parameters for a specific interaction are given in a
[pairtypes] directive. If these parameters are not present and "gen-pairs =
yes" then they are calculated. If parameters for a specific pair are not
present, and "gen-pairs = no" then grompp generates a fatal error.
3) Also am Icorrect about the normal nb-LJ coming from the [atom types
directive]
Yes.
4) I suppose a very obvious question would be; What is the difference
between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc)
A [*type] directive lists the parameters that should be a applied to whatever
interaction type might be found. For instance, a [bondtypes] directive contains
default parameters for all the bonds you might find, like C-C. If you then have
a [bonds] directive that lists:
; ai aj func
1 2 1
...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters
in the [bondtypes] directive and applies them to that bond, a process which it
carries out for all the rest of the interaction types, including pairs. If you
list specific pairs of atoms in a [pairs] directive, then grompp will search for
the appropriate parameters listed in a [pairstypes] directive. If none are
found, and "gen-pairs = yes," grompp generates the appropriate parameters for you.
-Justin
Gavin
P.S I appreciate you using your time to explain this
Justin A. Lemkul wrote:
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
========================================
--
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
