# Re: [AMBER] Steered MD calc

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 4 Jul 2010 19:16:27 -0400

Hello,

I can answer with fairly reasonable certainty 3 of the 4 columns, the 4th
column is only a (possibly educated) guess. The first column is the
equilibrium value of that constraint at that particular time step. The
second column is the ACTUAL value of the defined coordinate at that time
step. The fourth column is the amount of work done by the umbrella
potential.

The THIRD column, I'm not positive about. My guess would be that it's the
value of the force due to the umbrella potential at that point. This is
easy enough to check. Multiply the square of the difference 8.70127-5.3000
by your force constant and see if you reproduce -340012.6523. The negative
has to do with the fact that the actual value is greater than the
equilibrium value. Notice that when it swaps, and the actual becomes less
than the equilibrium value, the sign changes.

Hope this helps,
Jason

P.S. Perhaps this should be in the manual somewhere? Or in a more visible
spot. It's not entirely clear in the SMD section of the manual.

On Sun, Jul 4, 2010 at 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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```--
Jason M. Swails
Quantum Theory Project,
University of Florida