Hi,<br><br>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<br><br>[ nonbond_params ]<br><br>C OWT3 1 0.00335276 0.00000518<br>
CA OWT3 1 0.00266209 0.00000411<br>CC OWT3 1 0.00266209 0.00000411<br>CD OWT3 1 0.00266209 0.00000411<br>CE1 OWT3 1 0.00285525 0.00000481<br>CE2 OWT3 1 0.00280380 0.00000473<br>
CM OWT3 1 0.00365968 0.00000617<br>CP1 OWT3 1 0.00214019 0.00000506<br>CP2 OWT3 1 0.00307174 0.00000615<br>CP3 OWT3 1 0.00307174 0.00000615<br>CPA OWT3 1 0.00211808 0.00000227<br>
CPB OWT3 1 0.00211808 0.00000227<br>CPH1 OWT3 1 0.00157456 0.00000169<br>CPH2 OWT3 1 0.00157456 0.00000169<br>CPM OWT3 1 0.00211808 0.00000227<br clear="all">
... and so on<br><br>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.<br>
<br>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). <br>or this error<br>Fatal error:<br>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.<br>
<br>A simulation without this section runs fine.<br>Where could I have gone wrong? I have checked the calculations.<br>
<br>Pooja<br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>