Re: [AMBER] MD- the enzyme bouncing

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Mon, 14 Mar 2011 21:19:47 -0300

Inside VMD, for for the RMSDTT tool. It can align the frames of your molecule.

Gustavo.

On Monday, March 14, 2011, 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
>

-- 
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 14 2011 - 17:30:04 PDT
Custom Search