so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded?
On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham <[email protected]>wrote: > On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: > > Also, what about non-bonded interactions within the protein? Does exclusion > group only exclude the non-bonded interactions between two different > molecules and non-bonded interactions within the single molecule atoms are > still computed? > > > The sets of atoms for energy groups and such exclusions are defined by the > index groups, not molecules. See manual 7.3 and wherever it talks about > groups in an early chapter. > > > On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak <[email protected] > > wrote: > >> Hi >> >> When we define energy group exclusions e.g. like in manual energygrp >> excl = Protein Protein SOL SOL >> and do md rerun, then only non-bonded interactions between Protein and SOL >> are computed. I am wondering what happens to bonded interactions within the >> protein, do they contribute to energies even though we have excluded >> protein-protein interactions? >> > > Bonded interactions are unaffected, as you will see if you try it. > > Mark > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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