There's no a priori reason why a mixture of a united-atom detergent sodium dodecyl sulfate and an all-atom peptide *couldn't* work. Neither is there any reason to suppose they *would* work without evidence that the SDS parameters were developed with this purpose in mind and suitably validated. For that, you'll have to read the paper referred to on the page you footnoted [1], I guess. Your other alternative is looking for an all-atom SDS topology that has been validated, but I've no idea whether one exists.
Do you have any suggestions how one would validate the combination of two such force-fields? While generally one could always develop new parameters using the same methodology as the existing forcefield, it is not obvious how one would do this when combining all-atom and united-atom representations.
I see how the basic combination rules, etc. could be validated by simulating for example an aqueous protein restrained to one half of the simulation box and an SDS micelle restrained to the other half of the box in order to ensure no vdw contacts and then compare equilibrium properties from this simulation to those of an aqueous protein and an SDS micelle in separate simulations.
Further, in some situations one could look at the parameters to see the there are no striking differences between similar atom types. This would definitely be useful for example when trying to combine an all-atom protein forcefield with a united-atom forcefield. However, SDS doesn't really have any groups that are similar to and protein groups. Further, it is not readily apparent to me how one would even extend a protein forcefield using the same methodology to SDS and be sure based simply on methodology of generation that they were valid in combination since there is so little overlap in actual group types.
Thanks, Chris. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
