I just did 2 tests in first I do md rerun with SOL SOL exclusions along with PME option then I get forces on water atoms but in second case when I use Cut-Off for electrostatic forces are zero... not sure why PME introduces forces despite using energy exclusion group...
On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak <symasha...@gmail.com>wrote: > Also, in the case of spc/e bulk water when I do md rerun with SOL SOL > exlcusion I see forces on water atoms, however I was expecting it to be > zero. > > > On Tue, Apr 19, 2011 at 11:12 AM, Sikandar Mashayak > <symasha...@gmail.com>wrote: > >> 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 >> <mark.abra...@anu.edu.au>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 >>> <mark.abra...@anu.edu.au>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 < >>>> symasha...@gmail.com> 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 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 >>>> >>> >>> >>> >>> -- >>> 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 >>> >> >> >
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