Hello Everyone,
I have a question about solute movement out of the initial box. I have read
previous posts on this mailing list about this but I am not sure I perfectly
understand how this works.
I have a particular simulation with a small two residue solute that I am
able to simulate for over 200ns. I use iwrap=1 and upon visualization of the
trajectory I can see the solute at the edges sometimes.
Using the following ptraj commands
center :1 2
image familiar
The solute is in at the center for the duration of the calculation.
As I understand the commands above this should use the solute as center and
translate the solvent relative to this center.
I just want to be sure that this is correct and that I am not artificially
centering a solute that is not surrounded by water in the simulation.
My mdin looks like:
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 8, ntr = 0,
ntc = 2, ntf = 2,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000000, dt = 0.002, ig = -1,iwrap=1
ntpr = 500, ntwx = 500, ntwv = 500, ntwr = 1000
/
and I am using amber 10.
Thanks.
Emmanuel.
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Received on Mon Jun 28 2010 - 14:00:03 PDT
