[gmx-users] nonbond_params scaled for forcefield
saipooja at gmail.com
Tue Nov 2 02:23:08 CET 2010
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
On Mon, Nov 1, 2010 at 9:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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