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
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>
--
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
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Received on Mon Mar 14 2011 - 17:30:04 PDT
