[gmx-users] Fwd: How can i run my system successfully?

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================