thank you so I have to run different times !?
On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/15/15 9:12 AM, nazli kashani javid wrote: > >> Thank you very much. >> >> what do you mean of " multiple energy evaluations " ? >> >> do you mean I should change my .mdp file like this: >> >> energygrps = chaina chainb chainc chaind >> is it ok? >> >> > This will give you nonbonded energy decomposition of: > A-B > A-C > A-D > B-C > B-D > C-D > > e.g. all possible (non-redundant) combinations of individual chains. > > if I want to calculate interaction energy between ac and bd chains, what >> should I do? >> >> > Then you need groups that are chains AC and chains BD in two groups. > > -Justin > > > could you help me with more details about .mdp and .ndx files? >> >> On Sun, Feb 15, 2015 at 5:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/15/15 8:51 AM, nazli kashani javid wrote: >>> >>> Hi all >>>> I want to calculate interaction energy of my protein that includes 4 >>>> individual chains(a,b,c and d). at first I define an index file. It >>>> contains: >>>> [ chaina ] >>>> 1 2 3 4 ...454 >>>> [ chainb ] >>>> 455 456 457 ...919 >>>> [ chainc ] >>>> 920 921 922 .... 1373 >>>> [ chaind ] >>>> 1374 1375 1376 ....1838 >>>> [ chainsab ] >>>> 1 2 3....919 >>>> [ chainsac ] >>>> 1 2 3 ...454 920....1373 >>>> [ chainsad ] >>>> ...... >>>> [ chainsbc ] >>>> ..... >>>> [ chainsbd ] >>>> .......... >>>> [ chainscd ] >>>> ........ >>>> [ chainsabc] >>>> 1 2 3 .... 1373 >>>> [ chainsacd ] >>>> 1 2 3 .....454 920 ...1838 >>>> [ chainsabd ] >>>> ...... >>>> [ chainsbcd ] >>>> ........ >>>> >>>> I add these groups to .mdp file as following: >>>> >>>> energygrps = chaina chainb chainc chaind chainsab chainsac chainsad >>>> chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd >>>> >>>> when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n >>>> chains.ndx -o mda.tpr) , and face with this error : >>>> >>>> Fatal error: >>>> Atom 1 in multiple Energy Mon. groups (1 and 5) >>>> For more information and tips for troubleshooting, please check the >>>> GROMACS >>>> >>>> >>>> dose my index file need any modifications? is there any wrong with my >>>> mdp >>>> file? >>>> how could I solve my problem? >>>> >>>> >>>> You can't have overlapping groups. You'll have to do multiple energy >>> evaluations to achieve what you want. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.