[gmx-users] nonbond_params scaled for forcefield

[Justin A. Lemkul]

Sai Pooja wrote:
> Hi,
> 
> 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.

-Justin

> Pooja
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
> 

-- 
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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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