[gmx-users] nonbond_params scaled for forcefield

[Sai Pooja]

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.

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.

Pooja
-- 
Quaerendo Invenietis-Seek and you shall discover.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101101/f2ae8959/attachment.html>