Dear Amber users:
We are doing MD calculations with Amber 11 and sander.mpi on a quaternary system (disaccharides + 1 amino-acid + water) with PBC in order to study transport properties.
We did a 20.000 steps minimization combining Steepest Descent and Conjugate Gradient first keeping restrains and then 50.000 steps with the same combine methods without any restrain.
After that we did a 50 ps constant volume MD with the same restrictions used during the minimization. Then we released the restrictions and followed the MD at constant pressure in several 500ps runs.
We found that at the first run (of 500 ps) the average pressure lead to a high value. In the following runs this value rise fluctuating between 0.6 - 1.7 (the average) this value don't reach 1 even after 50 ns of running.
Here are the inputs:
Could anybody suggest us the possible reason for this behaviour, is it normal?
at NVT conditions:
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 8,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300,
ntt = 3,
gamma_ln = 2.0,
nstlim = 25000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
10.0
RES 145 170
END
END
at NTP conditions:
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, ig = -1, gamma_ln = 2.0,
nstlim = 250000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 5000
Waiting for a reply.
Regards,
Hernán Meier from Quitex Group UTN FRRe, Argentina
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Received on Thu Sep 22 2011 - 16:30:02 PDT
