Dear Amber members,
I performed SMD simulations and I found that the target (ion) didn't move(trajout the last frame of trajectory).
BUT,the output file seems it moves along the RC:
2.60000 2.57554 48.91815 0.00000
2.60000 2.57554 48.91815 0.00489
2.70000 2.69481 10.37240 -1.29598
2.80000 2.81560 -31.19316 -1.62172
2.90000 2.91381 -27.61897 -1.41272
3.00000 3.01436 -28.71035 -0.55049
3.10000 3.11332 -26.64870 0.63715
3.20000 3.17259 54.82269 1.84936
3.30000 3.32325 -46.50108 3.06072
3.40000 3.39271 14.57294 3.25384
3.50000 3.51021 -20.41882 3.19578
3.60000 3.64443 -88.86488 2.20332
3.70000 3.70403 -8.06447 1.29687
3.80000 3.78557 28.86179 1.52091
3.90000 3.88595 28.09795 2.97849
4.00000 3.97551 48.97474 5.56377
4.10000 4.08251 34.98008 9.47693
4.20000 4.18680 26.40166 14.64613
I dont know what's wrong.Below are input files.
The distance restraint file£º
&rst
iat=503,505,
r2=2.6,
r2a=4.6,
rk2=1000,#I know it seems too large .I just want to make sure the force big enough.
&end
SMD input file:
30 &cntrl
31 irest = 1, ntx = 5,
32 ntb = 2, pres0 = 1.0, ntp = 1,
33 taup = 2.0,
34 cut = 10.0,
35 ntc = 2, ntf = 2,
36 tempi = 300.0, temp0 = 300.0,
37 ntt = 3, gamma_ln = 2.0,
38 nstlim = $mdsteps, dt = 0.002,
39 ntwx = 1000, ntwr =20000, ntpr = 1000,
40 ig=-1, ioutfm=1,
41 irest = 0, jar=1,
42 /
43 &wt type='DUMPFREQ', istep1=1000 /
44 &wt type='END' /
45 DISANG=dist.RST.dat.1
46 DUMPAVE=asmd_$counter.work.dat.$stage
47 LISTIN=POUT
48 LISTOUT=POUT
I will very appreciate if anyone can offer some suggestions.
Look forward to your reply!
Best wishes.
wjli
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Received on Tue Apr 05 2016 - 07:00:04 PDT
