[gmx-users] nonbond_params scaled for forcefield
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 2 02:02:55 CET 2010
Sai Pooja wrote:
> Restating that I was trying to scale the Protein Solvent interactions, I
> added a new section to the ffnonbonded.itp file. This is what the
> section looks like
> [ nonbond_params ]
> C OWT3 1 0.00335276 0.00000518
> CA OWT3 1 0.00266209 0.00000411
> CC OWT3 1 0.00266209 0.00000411
> CD OWT3 1 0.00266209 0.00000411
> CE1 OWT3 1 0.00285525 0.00000481
> CE2 OWT3 1 0.00280380 0.00000473
> CM OWT3 1 0.00365968 0.00000617
> CP1 OWT3 1 0.00214019 0.00000506
> CP2 OWT3 1 0.00307174 0.00000615
> CP3 OWT3 1 0.00307174 0.00000615
> CPA OWT3 1 0.00211808 0.00000227
> CPB OWT3 1 0.00211808 0.00000227
> CPH1 OWT3 1 0.00157456 0.00000169
> CPH2 OWT3 1 0.00157456 0.00000169
> CPM OWT3 1 0.00211808 0.00000227
> ... and so on
> The C6 and C12 values were generated by using the sigma and epsilon
> values in the atomtypes section and then using Berthelot rules to get
> the sigma and epsilon for the interaction followed by conversion to C6
> and C12.
Which force field are you using? If this is related to your manipulation of
CHARMM, then conversion from sigma/epsilon -> C6/C12 is not necessary. The
CHARMM force field uses sigma/epsilon (combination rule 2).
> To test this new file, I started with a scaling factor of 1 but the
> simulation does not run after first 20 steps or so as the system
> explodes (LINCS warning).
> or this error
> Fatal error:
> 1 particles communicated to PME node 0 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> A simulation without this section runs fine.
> Where could I have gone wrong? I have checked the calculations.
Whatever you're doing is breaking the underlying physics of the force field,
most likely. Perhaps by weakening the intermolecular repulsion (which scales
with r^12), you're getting close contacts between the atoms in the system.
> Quaerendo Invenietis-Seek and you shall discover.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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