[gmx-users] fatal erroe in prorein-ligand comlex

[Justin Lemkul]

On 12/17/14 3:21 AM, Yaser Hosseini wrote:
> hi
>
> thank you for your replay dear justin
>
> after that error i can solve it with your help i got one more fatal error
> in nvt step , i do every thing that you said in your tutorial but i cant
> pass this step:
>
> mdrun deffnm nvt
>
> error:
>
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
> step 0
> Step 14, time 0.028 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.009678, max 0.394560 (between atoms 5800 and 5799)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     5800   5799   87.7    0.1140   0.1590      0.1140
>     5801   5800   57.0    0.1430   0.1569      0.1430
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

Also Google the error and you will turn up the million or so posts in which 
people have asked the same question and gotten advice.

-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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