Yes, 7.3.19 says that all non-nonbonded interactions are excluded within energy_exclusion groups.
What I really trying is to get forces on water atoms only because of water water interactions and I want force on protein atoms to be zero, so I do md rerun with energy_exclusion as PROTEIN PROTEIN PROTEIN SOL and also remove any bond interaction information from .top file for protein, but still I get force values on protein atoms. Not sure whats going wrong? thanks sikandar On Tue, Apr 19, 2011 at 12:04 AM, Mark Abraham <[email protected]>wrote: > On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: > > 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? > > > What does manual 7.3.19 say? > > Mark > > > 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 >> > > > > -- > 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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