On 12/7/13 4:51 AM, bahareh khanoom wrote:
Dear friend thanks for your answer first i generate" DRG.itp" for adsorbed molecules, by PRODRG server. next i optimize adsorbed moleculs by gaussian b3lyp/6-311++g(d) opt Pop=ChelpG and the end ,i replaced the charges in" DRG.itp" with charges that produced by gaussian.
How do these charges compare with existing charges for similar functional groups in the force field? AFAIK, there is no hard evidence as to which QM method will give the best results from Gromos96 force fields.
so ,what is the reason?
It is hard to say at this point, but one solution is to simulate each component individually to verify that their topologies are correct and that your .mdp settings are appropriate (though they look reasonable on first glance).
See also http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.