[gmx-users] use of SW.itp...
Dennis Sprous, PhD
dsprous at bioleap.com
Mon Jul 25 18:41:20 CEST 2011
I am trying to make use of polarizable water models.
I have attempted to employ the Maaren & van der Spoel [2001. JPC
105:2618] model embodied by the sw.itp embedded in share/gromacs/top. I
encountered the following issues:
1. the lines:
; [ defaults ]
; LJ Geometric
where duplicated from my main *.top file. Hence I commented these out.
2. The atom types WO, WH, WS and WD were not in oplsaa, so I appended
them to the file oplsaa.ff/ffnonbonded.itp.
3. The atom WS (the shell atom) -- but not WD -- requires a mass to
which I set to a minimal value in the itp file:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 WO 1 SM OW1 1 1.24588
2 WH 1 SM HW2 1 0.62134 1.008
3 WH 1 SM HW3 1 0.62134 1.008
4 WD 1 SM DW 1 0.0 0.000
5 WS 1 SM SW 1 -2.48856 0.008
Before I start some MD, did I do anything against good practices here?
any problem worth attack
proves its worth by fighting back
Piet Heins "Grooks"
D.G. Sprous, PhD
Cambridge MA 02141
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