Gavin Melaugh wrote:
Hi all
A very quick question. I have an atom-type labelled CH in the atom-types
with a particular charge, and in the atom list I assign some of these
specific atoms with zero charge as below. When I generate 1,4
interactions using gen_pairs =yes, what charge for the CH type does it
use? Does gromacs assign the CH with the different charge as a new atom
type.
Charges set in [atomtypes] are not used. The zero charge is assigned. Verify
this by using gmxdump on your .tpr file.
-Justin
;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
;Molecular level
[moleculetype]
; name nrexcl
isotridecylcage 3
[atoms]
.................
72 CH 1 CGE CH 24 0.3320 13.0190
73 C2 1 CGE C2 25 0.0000 14.0270
74 C2 1 CGE C2 25 0.0000 14.0270
75 C2 1 CGE C2 25 0.0000 14.0270
76 C2 1 CGE C2 26 0.0000 14.0270
77 C2 1 CGE C2 26 0.0000 14.0270
78 C2 1 CGE C2 26 0.0000 14.0270
79 C2 1 CGE C2 27 0.0000 14.0270
80 C2 1 CGE C2 27 0.0000 14.0270
81 C2 1 CGE C2 27 0.0000 14.0270
82 C2 1 CGE C2 28 0.0000 14.0270
83 CH 1 CGE CH 28 0.0000 13.0190
84 C3 1 CGE C3 29 0.0000 15.0350
Many Thanks
Gavin
--
========================================
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
