Hi all experts,
I have problem with visualisation of trajectory of protein - ligand
production in explicit solvent in VMD, namely during simulation ligand
is suddenly going outside the binding site and after few hundreds steps
it returns and stay there. It seems to be shifted to other picture by a
vector. There is no rotation at the time when ligand is outside, which
should occur for reliable simulation results. For these reasons I
suppose this is a visualisation problem.
Input file attached. Please give suggestions.
Thanks,
Maciek
&cntrl
imin = 0, irest = 1, ntx = 5, ig = -1,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 12.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 18000000, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 10000,
iwrap = 1, ioutfm = 1,
/
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Received on Wed Jan 10 2018 - 04:00:03 PST
