[gmx-users] Umbrella Sampling problem

[Justin Lemkul]

On 6/23/15 10:19 PM, Lin wrote:
> Dear all,  I follow the Umbrella Sampling tutorial, and have some problems:
> 1. pdb2gmx with -ter have warning "TYR-1 missiong H"

So you have missing atoms or an incorrect terminus selection.  The tutorial caps 
the N-terminus with an ACE group; if you haven't done that then you shouldn't be 
doing the same thing.

> 2. grompp -f npt_umbrella.mdp  have 1 warning, but I avoid it.

Well that sounds like a terrible idea.  What does "avoid" mean?  What was the 
warning?  Do you know why grompp told you there was a problem?

> 3. Gromacs 4.6.7 and gromacs 5.0.4 have same result: energy minimum is 24.8 kcal mol-1So, what happed in my simulations ?  The result is wrong or not ? and how can I do?Thanks! 		 	   		
>

Depends on if your topology is broken (per point 1) or if you have bypassed some 
important problem in the input settings (point 2).

-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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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