Re: Accelerated MD

From: Thomas Albers (talbers_at_binghamton.edu)
Date: Wed Aug 29 2012 - 16:20:50 CDT

Dear Jeff,

> In general choosing your parameters can take some trial and error. For the
> amber force field we do have a rule of thumb that might be helpful.

> E_dihed=V_d+4*Nres
> alpha_dihed=4*Nres/5
>
> And for the total you could try:
> E_tot=V_tot+N_atom/5
> alpha_tot= N_atom/5

I have seen these recommendations - but unfortunately they are geared
to proteins in waterboxes, not proteins in membranes. It seems there
is not much experience yet with systems in membranes.

As far as the torsional boost goes, it's hopefully not too far off to
consider each lipid molecule equivalent to 8 residues. In a waterbox,
the average torsional energy is 134.44 kcal/mol; in a membrane the
average torsional energy is 4070.72 kcal/mol. This is a 36-peptide,
84 POPC lipids, total number of atoms ~30000.

> You should see an increase in the total potential energy of the
> system, especially the non-bonded values. Could it be that you just
> set your E_tot value too low?

It's possible. aMD requires no knowledge about the reaction
coordinate - the rub is it does require an idea about the shape of
your energy surface.

> Perhaps you could post the aMD segment
> of your input file, and a line from the log file listing your
> energies?

Classical:
ETITLE: TS BOND ANGLE DIHED IMPRP
          ELECT VDW BOUNDARY MISC KINETIC
          TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
       PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 2500000 1348.0388 6963.5112 4091.9386 52.2924
    -75387.6076 1587.5850 0.0000 0.0000 18701.9533
    -42642.2883 297.6219 -61344.2416 -42515.9520 299.1962
       -61.4966 -10.6912 280397.9540 -10.2274 -11.2790

aMD:
Info: APPLYING DUAL BOOST
Info: accelMDE: 6900 KCAL/MOL, accelMDalpha: 570 KCAL/MOL
Info: accelMDTE: -37700 KCAL/MOL, accelMDTalpha: 4690 KCAL/MOL
..
ETITLE: TS BOND ANGLE DIHED IMPRP
          ELECT VDW BOUNDARY MISC KINETIC
          TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
       PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 4255000 1285.5574 6930.1107 6428.2382 72.8927
    -75149.9582 1573.5278 0.0000 0.0000 18908.0391
    -39951.5923 300.9158 -58859.6314 -39827.3616 301.5948
      -295.7028 -272.8425 281407.1178 5.2652 5.2668

Thomas

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