Hi, Iīm trying to perform steered molecular dynamics on system
simulating a decomplexation process. I wrote an input file quite
similar to the one that shows the manual, in order to move atoms 166
and 92 from their initial distance (X) to 6 A. Here is the complete
input file i used:
Monitoring steered molecular dynamics for the complex cydr_1
&cntrl
igb = 0, ntx = 1,
ntb = 0, ntp = 0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
ntf = 2, ntc = 2, tol = 0.00001,
cut = 12.0, dt = 0.002,
ntpr = 5, ntwx = 0, nstlim = 10000
/
ncsu_smd
output_file = 'smd.txt'
output_freq = 50
variable
path= (X, 6.0)
harm = (10.0)
type = DISTANCE
#list of participating atoms
i = (166, 92)
#reference coordinates
r = (-17.752, 5.695, -26.272, -17.216, 8.476, -25.557)
end variable
end ncsu_smd
The problem is that i donīt get nor a mdcrd file, neither the smd.txt
results file, so i don't really know what i'm doing wrong...I would
appreciate any help you could give me.
Thanks,
Edu
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Received on Thu Oct 21 2010 - 08:30:05 PDT
