Dear amber users:
I used SMD to apply an external force between two atoms.
after md1 for equiblirum I will run md2 input file:
I use Amber10 manual(page 111&112)
but it give below eror:
*Cannot match namelist object name ’dumpfreq’
Cannot match namelist object name ’end’
Cannot match namelist object name ’dumpfreq’*
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 = 4000, 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
my dist.RST file is:
*# Change distance between atoms 943 and 1 from 30 A to 50.0 A
&rst iat=943,1 , r2=30., rk2 = 5000., r2a=50.0, /*
* Please kindly help. *
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Received on Tue May 08 2012 - 09:00:02 PDT
