Gavin Melaugh wrote:
Hi Justin
Sorry to labour on this but:
I don't quite understand what you mean when you say that nonbonded pair
interactions are not Coulombic. Surely nonbonded charged atoms interact
with each other, when close enough? (or by Nonbonded pair interactions
do you explcitly mean 1-4,1-5, etc.)
What are the 1-4 Coulombic interactions generated by, if not by
gen_pairs =yes in my case?
I have read this section of the manual loads and though I had a
comprehensive understanding of it, but now I am confused again.
Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the purpose of
[pairtype] generation is for LJ terms only. They are special 1-4 interactions
between different atomtypes. Look at any force field for which [pairtypes] are
listed - they have only C6 and C12 terms. Charges are not used for these
calculations, but they are applied later during the MD using normal Coulombic
equations and FudgeQQ.
-Justin
Thanks
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
I have checked the tpr file. Now it seems to assign the the two type of
CHs as the same atom type, but at the same time with the specified
charge from the [atoms] directive, as I expected. Concerning 1-4
interactions and gen_pairs =yes, my concern is this; from the pair list
and using gen_pairs = yes, does grompp then take the 1-4 coulombic
interaction for CH from the [atomtypes] directive (as the meaning of
gen_pairs =yes)?
Or does it assign the charge based on the atom index in the pair list?
Charges are irrelevant for generation of pair interactions. Nonbonded
pair interactions are LJ, not Coulombic. You will certainly have 1-4
Coulombic interactions, but they are not generated by gen_pairs. See
manual section 5.3.4.
-Justin
Many Thanks
Gavin
Justin A. Lemkul wrote:
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
========================================
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