Dear Thomas,
Thanks for your comments. Actually, No, I have not used ptraj to image it
back, I will look through the tutorial/manual to know how to do that then
get back to you! thanks
Best wishes
Mahmoud
On 3/28/11 4:05 PM, [1]steinbrt.rci.rutgers.edu wrote:
Hi,
are you sure this isn't just the usual neighbouring box diffusion problem?
Did you look at your raw trajectory or did you use ptraj to image it back
into the original box before visualisation?
Thomas
On Mon, March 28, 2011 10:02 am, Mahmoud Soliman wrote:
Hi Amber users,
However, I am doing NVT simulationsI notice that my TIB3P box deforms
during MD simulations, any idea?? below is my input file
QM/MM equilibration NVT with some restraints on the solute for 100ps
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
taup = 2,
cut = 10,
tempi = 100.0, temp0 = 300.0,
ntc=2,
ntf=2,
ntt = 3,
tol = 0.0001,
iwrap = 1,
ntt = 3,
gamma_ln = 1.0,
scee= 1.2,
nstlim =50000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
ntr = 1, restraint_wt=2.0, restraintmask=':1-186',
ifqnt=1
/
&qmmm
iqmatoms=
1132,1133,1134,1135,1136,1137,2582,2583,2584,2585,2586,2587,2588,2772,2773,2774
,2775,2776,2777,2778,2779,2780,2781,2782,2783,2784,2785,2786,2787,2788,2789,279
0,2791,2792,2793,2794,2795,2796,2797,2798,2799,2800,2801,2802,2803,2804,2805,28
06,2807,2808,2809,2810,2811,2812,2813,2814,2815,2816,2817,2818,2819,
qmcharge=-1,
qm_theory='AM1',
qmcut=8.0,
writepdb=1
qmshake=0,
/
Thanks
Mahmoud
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Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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[5]
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--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[6]
http://people.bath.ac.uk/mess20/
[7]
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:
[8]mess20.bath.ac.uk
[9]meelkot.zu.edu.eg
[10]mahmoudelkot.gmail.com
References
1. mailto:steinbrt.rci.rutgers.edu
2. mailto:AMBER.ambermd.org
3.
http://lists.ambermd.org/mailman/listinfo/amber
4. mailto:AMBER.ambermd.org
5.
http://lists.ambermd.org/mailman/listinfo/amber
6.
http://people.bath.ac.uk/mess20/
7.
http://www.bath.ac.uk/person/812559
8. mailto:mess20.bath.ac.uk
9. mailto:meelkot.zu.edu.eg
10. mailto:mahmoudelkot.gmail.com
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Received on Mon Mar 28 2011 - 09:00:05 PDT
