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 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

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