AMBER Archive (2004)

Subject: RE: AMBER: minimization output file format

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 12 2004 - 14:43:02 CDT

Dear Marsita

> with the meanings of the minimization output file, such as:

No problems, have you worked through the tutorials on
http://amber.scripps.edu/tutorial/index.htm these are good introductions to
Amber.

> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -1.3419E+04 1.7043E-01 1.6570E+01 CG
> 1012
>
> BOND = 281.5388 ANGLE = 1182.3429 DIHED
> = 5309.2460
> VDWAALS = -2823.1990 EEL = -33036.8393 EGB
> = -10465.3807
> 1-4 VDW = 1610.5875 1-4 EEL = 25129.8490 RESTRAINT
> = 0.6661
> ESURF = 292.5711
> EAMBER = -12519.3177
>

Ok, NSTEP is the step number so above is step 100 of the minimisation. Note
amber does not by default print every step but prints every NTPR steps as
set in the input file (default - 50). Energy is the total energy of the
system, as determined from the force field equation, in Kcal/mol. RMS is the
mean of the square root of the dot product of the force vectors. This should
decrease as you system approaches the minima. GMAX is the magnitude of the
largest component of the force vectors, I.e the largest force and NAME and
NUMBER are the atom that has that largest force. I.e the one that will move
the most during the minimisation step.

Everything below that are the individual energy components from the force
field equation. If you add these all up they should sum to the value
reported under ENERGY. The total energy should decrease as you minimise your
system. The energies are all in Kcal/mol, the forces are in Kcal/mol/A

> my second question is... is it common/ok to use both implicit
> and explicit
> simulation for one system? say like.. for the minimization, i
> want to use
> explicit MD, and the equilibration part, i would wish to use
> both implicit
> and explicit MD simulation (say 20 ps implicit, and another
> 1ns explicit)..
> is it acceptable to do that ? hope to hear from any of you.. thanks

Ideally if you are going to run a simulation in explicit solvent you should
minimise in explicit solvent, if you are going to run in implicit solvent
you should minimise in implicit solvent. You may get away with minimising in
explicit solvent, removing your minimised protein and then running MD with
implicit solvent but considering how little time the minimisation takes
compared to the MD you might as well minimise both systems seperately unless
there some specific difference you want to show between the implicit and
explicit models.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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