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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Received on Mon Mar 14 2011 - 14:00:02 PDT
