Dear all
I used Umbrella Sampling in MD file.
I used Amber10 manual(page 111&112)
my MD file is:
*DNA 15-mer: 8ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
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 = 1000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
jar=1,
/
&wt type= "DUMPFREQ", istep1=1 /
&wt type="END" /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT*
and dist.RST file is:*
# Change distance between atoms 943 and 1 from 17 A to 30.0 A
&rst iat=943,1 , r2=17., rk2 = 5000., r2a=30.0, *
but output is only one line that is:
17.00000 17.59934 -5993.44359 0.00000
But change in distance is not performed.
I would appreciate your help.
Looking forward to hearing from you.
Best regards
M.Bagherpour
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Received on Thu May 10 2012 - 01:00:05 PDT
