nishap.pa...@utoronto.ca wrote:
Hello,
I created a topology file for 1 ammonia in water. Could someone
please have a look at the file and let me know if it looks okay.
With a fractional charge of +0.38, I'd say these parameters (at least as far as
the charges) are inappropriate. The only way to determine if parameters are
appropriate is to derive them in a manner consistent with the original force
field. This is not a trivial task. Consult the list archive and Gromacs wiki
for tips.
-Justin
Thanks
Nisha Patel
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Ammonia 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_237 1 NH3 N 1 -0.76 14.0067 ;
qtot -0.76
2 opls_240 1 NH3 H1 1 0.38 1.008 ;
qtot -0.38
3 opls_240 1 NH3 H2 1 0.38 1.008 ;
qtot 0
4 opls_240 1 NH3 H3 1 0.38 1.008 ;
qtot 0.38
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1
2 1 4 1
3 1 4 1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
[ system ]
; Name
ammonia in water
[ molecules ]
; Compound #mols
Ammonia 1
SOL 345
--
========================================
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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