On 30/03/2010 1:57 AM, Gavin Melaugh wrote:
Hi guys
Sorry about the wrong subject in the previous e-mail. (I just hit reply).
It's preferable to start a new email entirely. Archival software
sometimes uses the information in email headers, which might not match
up properly if people start emails from the middle of other discussions'
threads.
I have been running gromacs for a few months now with no real problems
however some of my numbers differ from my supervisor's who uses DL-POLY.
Anyway discussion of the discrpnacies has led me to questioning aspects
of my topology file below (exerpts). We created the topology ourselves.
I always thought that the set up below would calculate 1-4 interactions,
but having read through the archives I am now confused. Do I have to
give a pair list in topology file, or is gen-pairs = yes sufficient. I
never created a pairlist as I thought that gen-pairs would create it
from the parameters in atomtypes.
The example in manual section 5.7.1 seems to describe the use of
gen_pairs well enough. 5.3.4 may also help. You need to be clear about
which force field you are using and how its parameters are expected to
be combined to produce 1-4 interactions. You haven't given us enough
information to help with that...
;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)
CB 12.011000 0.000000 A 0.355000 0.292880
CA 12.011000 -0.115000 A 0.355000 0.292880
HC 1.008000 0.115000 A 0.242000 0.125520
CU 13.019000 0.265000 A 0.350000 0.334720
NU 14.007000 -0.597000 A 0.325000 0.711280
CH 13.019000 0.332000 A 0.385000 0.334720
C3 15.035000 0.000000 A 0.390500 0.732200
C2 14.027000 0.000000 A 0.390500 0.493712
;Molecular level
[moleculetype]
; name nrexcl
subhexylcage 3
[atoms]
; atomnr type resnr residue name cgnr charge mass
1 CA 1 CGE CA 1 -0.1150 12.0110
2 CB 1 CGE CB 1 0.0000 12.0110
If this is your topology, you have much bigger problems than pairlists.
You have only two atoms defined such that your molecule has a net
partial charge. If you're exerpting stuff, please indicate that explicitly.
Mark
[bonds]
; ai aj func b0(nm) kb(kjmol-1 nm-2)
1 2 1 0.1400 392459.2
1 6 1 0.1400 392459.2
[angles]
; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2)
2 1 6 1 120.00 711.2800
2 1 7 1 120.00 292.8800
[dihedrals]
; ai aj ak al func V1 V2
V3 V4 (all kj mol-1)
1 2 3 4 5 0.00000 30.33400
0.00000 0.00000
1 2 3 10 5 0.00000 30.33400
0.00000 0.00000
;System level
[system]
;the name of this system
config test of 32 subhexyl cage molecules
[molecules]
; moleculename number
subhexylcage 32
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