Hi, I'd like to perform TI calculations as described in section 3.12.2 of the (version 4.5.4) manual. my questions are:
1) i understand in Gromacs TI/FEP is implemented as a single topology, and not dual topolgy algorithm, is that correct? 2) to successfully analyze the results with BAR what is a good frequency at which i would save energies and dU/dlambda values? 3) how do i set up topologies in practice? If for example i wanted to mutate an ASN to a PHE residue in solution I seem to have at least two options: a) a direct mutation, where i'd mutate, e.g., CD1 and CD2 in PHE to OD1 and ND2 respectively in ASN, and so forth, including a transformation of a few PHE atoms to dummies, and a transformation of some bonded energy terms. b) construct a bastard residue from a PHE and a ASN residue, where the two residues share the backbone atoms, including C-alpha, but where there are two full and different copies of the side chain - and then mutate from state A with all sidechain atoms of, say, ASN set to dummies and the PHE atoms fully turned on, to state B (vice versa) ... this would be like emulating a of dual topology approach, wouldn't it? is there any good reason for using either a or b? To me option a seems to be the more tedious one as i'd have to include the changes in bonded energy terms by hand into the topology file, while with option b pdb2gmx and grompp would do most of that work for me, correct? Also if i used option a then at the ASN state would I not get some spurious effects from the ring topology of PHE, from the PHE atoms that have their non-bonded interactions turned off but their bonded interactions are still there?? (i seem to recall that totally turning off any bonded interactions opens a can of worms) thanks in advance for any help! cheers Michael -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
