[gmx-users] nonbond_params scaled for forcefield

[Sai Pooja]

Thanks Justin.The simulation is indeed with CHARMM and the error went away
when I used sigma and epsilon instead of C6 and C12. This run was for no
scaling but now I can design the rest of the simulation without scaling the
C12 term.

Thanks again
Pooja

On Mon, Nov 1, 2010 at 9:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

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