On 05/11/2011 02:04 AM, Gavin Melaugh wrote:
Hi again
To rephrase. If I have two atoms constructing a charge group, is it not
possible to have one of these atoms constructing an energy group on its own?
Correct. Neighbour lists are constructed from the set of whole charge
groups in each energy group, as the error suggests.
Mark
Cheers
Gavin
Gavin Melaugh wrote:
Hi All
I have set up a topology file and with virtual sites (exerpts below),
whereby my virtual sites only interact with the C3 atoms. I am trying to
construct a PMF wrt one particular C3. This atom I do not want to
interact with the virtual sites at all. I thought the best way to do
this was via energy exclusion groups. So I set up some groups in the
index file (see below), and defined the energy groups like so
energygrps = vsites vsitex
energygrp_excl = vsites vsitex
but I get the following error
Fatal error:
atoms 415 and 416 in charge group 89 of molecule type 'name' are in
different energy groups
I have no charge group 89 in my molecule. Can someone please suggest
where I might be going wrong.
;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 0.391000 0.669440
C2 14.027000 0.000000 A 0.390500 0.493712
VS 0.0 0.0 V 0.0 0.0
[nonbond_params]
;i j funct sigma epsilon
VS C3 1 0.1 0.03153
[ cage_1 ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 75 89 103 117 131 145 159 173 187 201 215
[ tail ]
416
[ vsites ]
229 230 231 232 461 462 463 464
[ vsitex ]
416
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