On 4/20/2011 4:14 AM, Sikandar Mashayak wrote:
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...
Because that's how PME works. Part of the electrostatic non-bonded contribution is done in reciprocal space, and that can't be readily decomposed into group-wise contributions.
Mark
On Tue, Apr 19, 2011 at 11:39 AM, Sikandar Mashayak <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[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? MarkOn Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham <[email protected] <mailto:[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] <mailto:[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] <mailto:[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] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing list [email protected] <mailto:[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] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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