Dear Amber Users,
i am doing the MD simulations for organic molecules
with periodic boundary conditions. i have used the follwing input for
the MD simulation.
MD_simulation of IMB in PBC_1
&cntrl
imin = 0, irest = 0, ntx = 1,
ntt = 1, temp0 = 10.0, tautp = 1, gamma_ln = 10000,
ntp = 0,
ntb = 1, ntc = 1, ntf = 7,
nstlim = 10000,
tempi = 0.0, dt = .0005,
cut = 20.0, scee = 4.0, scnb = 20.0,
ntr = 1, ntpr = 100, ntwx = 100,
&end
&ewald
nbflag = 0,
&end
keep PIB fixed with strong constraints
100
RES 1 64
END
END
during the mD run, i am getting lines (extended C-H, C-C, C-O bonds from
one end of the box to the other end of the box).
is it due to the less simulation time period or the effect of box size
or the effect of some other parameters.
could anyone clear this problem.
thanks...anand
ANANDA RAMA KRISHNAN .S
PhD Student
c/o. Prof. Rudolf Friedemann
Department of organic chemistry
Martin Luther university
Kurt-mothes-str.2
D-06120 Halle (saale),Germany
e-mail: ananda.selvaraj.chemie.uni-halle.de
Ph(lab) : (+int) 345 - 5525683
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Received on Tue Jun 14 2005 - 17:53:01 PDT
