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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