Try aligning the system (using RMS in whichever viewer you're using).
Molecules naturally translate and rotate during dynamics, and Amber
automatically removes COM translation every once in awhile, which may cause
what you're seeing.
Good luck,
Jason
On Mon, Mar 14, 2011 at 1:44 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Dear Guys,
> I am running MD simulation for an enzyme in implicit solvent and I am
> using
> the input below. When I visualize the trajectory using VMD or Chimera I
> see
> the enzyme (whole molecule) is moving everywhere in the screen, any
> reason
> why is that happening, is there anything wrong in the input file????
> Equilibration MD of the system for 5ns no restraints
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 7,
> ntb = 0,
> igb=5,
> pres0 = 1.0,
> taup = 2,
> cut = 10,
> ntr =0,
> tempi = 300.0, temp0 = 300.0,
> ntc=2,
> ntf=2,
> ntt = 3,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim =2500000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
> /
> thanks
> Mahmoud
>
> --
>
> *************************************************
>
> Mahmoud E. Soliman
>
> Computational Chemistry & Modeling (PhD)
>
> Department of Chemistry
>
> University of Bath
>
> Bath
>
> BA2 7AY
>
> United Kingdom
>
> [1]http://people.bath.ac.uk/mess20/
>
> [2]http://www.bath.ac.uk/person/812559
>
>
> *********************************************
>
> Mahmoud E. Soliman
>
> Lecturer of pharmaceutical organic chemistry
>
> Pharmaceutical Organic Chemistry Dept.
>
> Faculty of pharmacy
>
> Zagazig University
>
> Zagazig
>
> Egypt
>
> **********************************************
>
> Email:
>
> [3]mess20.bath.ac.uk
>
> [4]meelkot.zu.edu.eg
>
> [5]mahmoudelkot.gmail.com
>
> References
>
> 1. http://people.bath.ac.uk/mess20/
> 2. http://www.bath.ac.uk/person/812559
> 3. mailto:mess20.bath.ac.uk
> 4. mailto:meelkot.zu.edu.eg
> 5. mailto:mahmoudelkot.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 14 2011 - 15:30:04 PDT
