where did you get the atom numbers you used ? (503 and 505)?
If they came from vmd, please note that vmd (depending if you use index
or others ways), will be off by one from the amber count.
Basically, you are clearly moving two atoms, just not the two you want
to move.
adrian
On 4/5/16 9:56 AM, wjli wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Apr 05 2016 - 07:30:03 PDT
