Dear Amber community,
I have conducted the simulations following the tutorial B1 - Section 5 with
ntb = 1 and igb = 0. I also specify the box dimensions using the following
command.
set mybox box {300.092, 300.141, 300.087}
However, the box dimensions are still changing. Could you please, provide
any way.
Please let me know, if need top/crd and input files.
thank you
Dear amber community,
I performed MD simulations on a box of dimension 300 x 300 x 300. I defined
the dimensions using the following command.
setbox mybox vdw
I noticed that, as MD simulations proceed, the box dimension are changing.
My first frame has the following dimension, generated by vmd.
min1 = (1.2740000486373901, 1.4450000524520874, 1.0440000295639038)
max1 = (302.4549865722656, 302.99700927734375, 302.3590087890625)
total = ( 301.181, 301.552, 301.315 )
and the final frame has the following dimensions after completing 125000
steps.
min2 = Vector(1.371000051498413, -6.394000053405762, -1.9179999828338623)
max2 = Vector(305.86700439453125, 305.4129943847656, 306.697998046875)
total= ( 304.496, 311.807, 308.616 )
If I perform additional 10times steps, the dimension keeping changing to a
very large number. Could any one please guide me how I can keep the
dimensions fix to 300x300x300 throughout the simulations.
Here is my MD script.
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100, ntwr = 8000
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 125000, dt = 0.001,
cut = 999
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Received on Mon May 16 2016 - 09:00:10 PDT
