There are a number of different issues with your email.
First, SMD can NEVER tell you what force will be needed to separate two
molecules. This is misunderstanding of the process. As an example, ZERO
force will also separate two molecules, but it might take a long time to
do so. A larger force will separate them faster (on average), but there
is no single force that can be pointed to as 'the force'.
As for the output, the first column is the target distance (what you
WANT IT TO BE at each time), the second is what the distance IS at that
same time, the third is the force, and the 4th column the work
accumulated so far.
Note that the first line in your system wants to be at 5.3 angstroms but
it is in fact at 8.70127
I do not know how you choose 5.3 to start, but I strongly recommend that
you run a long equilibration with a restraint fixed at 5 A before trying
to pull to 20 A.
Adrian
On 7/4/10 12:24 PM, eduardo.troche.uvigo.es wrote:
> Hi amber users!
> I've made some steered molecular dynamics calculations in order to
> know the force that will be needed to separate two molecules that form
> an inclusion complex, taking two atoms as reference,that are separated
> from 5 A, till they reach 20 A, but i don't really understand the
> output file dist_vs_t....could anybody tell me what corresponds to
> each column?i put the first lines of the file...
>
> 5.30000 8.70127 -34012.65230 0.00000
> 5.30000 8.70127 -34012.65230 -4.99986
> 5.30015 8.56117 -32610.20110 -9.89664
> 5.30029 8.36929 -30689.93773 -14.54920
> 5.30044 8.13395 -28335.13996 -18.88754
> 5.30059 7.85851 -25579.22092 -22.85025
> 5.30074 7.56148 -22607.41418 -26.39197
> 5.30088 7.23016 -19292.78238 -29.47163
> 5.30103 6.88039 -15793.61850 -32.05048
> 5.30118 6.54024 -12390.62704 -34.12202
> 5.30132 6.23016 -9288.33970 -35.71543
> 5.30147 5.96226 -6607.94570 -36.88380
> 5.30162 5.73175 -4301.33170 -37.68564
> 5.30176 5.51988 -2181.15481 -38.16210
> 5.30191 5.33087 -289.56712 -38.34370
> 5.30206 5.21257 894.86571 -38.29921
> 5.30221 5.21246 897.46395 -38.16747
> 5.30235 5.35556 -532.08631 -38.14062
> 5.30250 5.49030 -1878.00275 -38.31776
> 5.30265 5.34431 -416.60482 -38.48641
> 5.30279 5.14417 1586.23007 -38.40044
> 5.30294 5.19599 1069.50687 -38.20525
> 5.30309 5.44326 -1401.73477 -38.22967
> 5.30323 5.45307 -1498.34484 -38.44282
> 5.30338 5.21921 841.73523 -38.49108
> 5.30353 5.15093 1525.97424 -38.31706
> 5.30368 5.33938 -357.02551 -38.23114
> 5.30382 5.47767 -1738.48633 -38.38516
> 5.30397 5.36381 -598.43253 -38.55692
> 5.30412 5.17359 1305.23185 -38.50497
> 5.30426 5.15824 1460.23572 -38.30171
> 5.30441 5.32239 -179.79009 -38.20760
> 5.30456 5.46372 -1591.65530 -38.33780
> 5.30470 5.44022 -1355.19975 -38.55439
> 5.30485 5.27816 266.88087 -38.63438
> 5.30500 5.15611 1488.85558 -38.50534
> 5.30515 5.23412 710.29534 -38.34370
>
> Thank you very much
>
>
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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Sun Jul 04 2010 - 20:30:04 PDT
