AMBER Archive (2007)

Subject: RE: AMBER: QM-MM output interpretation

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jul 30 2007 - 12:59:13 CDT

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

Hi Ross:

> No in so much that you are trying to do the wrong type of analysis. The
> average potential energy may be of use but it really depends on what you
> want to observe.

A V E R A G E S O V E R 1000 S T E P S

Conformer 1eq QM-MM

 NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 307.61 PRESS = 0.0
 Etot = -22861.3789 EKtot = 5977.6905 EPtot = -28839.0694
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 4125.6242
 EELEC = -32704.9171 EHBOND = 0.0000 RESTRAINT = 0.0000
 PM3ESCF= -259.7765
 Ewald error estimate: 0.3833E-01

Conformer 1eq Classical

NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 306.29 PRESS = 0.0
 Etot = -22608.2739 EKtot = 5951.9683 EPtot = -28560.2422
 BOND = 19.1565 ANGLE = 84.9878 DIHED = 98.6041
 1-4 NB = 35.1291 1-4 EEL = -46.8335 VDWAALS = 4140.5998
 EELEC = -32891.8861 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1105E-03

Conformer 2ax QM-MM

 
 NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 307.13 PRESS = 0.0
 Etot = -23264.0985 EKtot = 6080.0172 EPtot = -29344.1157
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 4175.6245
 EELEC = -33262.5509 EHBOND = 0.0000 RESTRAINT = 0.0000
 PM3ESCF= -257.1894
 Ewald error estimate: 0.3883E-01

Conformer 2ax Classical

NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 306.29 PRESS = 0.0
 Etot = -23046.3462 EKtot = 6063.3542 EPtot = -29109.7005
 BOND = 19.4265 ANGLE = 86.8701 DIHED = 100.7738
 1-4 NB = 33.6520 1-4 EEL = -45.9211 VDWAALS = 4235.2760
 EELEC = -33539.7779 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1004E-03

Judging from QM-MM PM3ESCF, a difference of 2.59 kcal/mol between the two
conformers is not too far from the experimental value (NMR) of ca 1.9. Though -
after what you explained in detail for this type of system - is that average
/\PM3ESCF an estimate on which to rely?

>A 'traditional' option would be, if you don't want any
> dynamic information, would be to minimize the two structures and compare the
> potential energies for the minimum's. However, this would be at 0K and would
> not necessarily apply at room temperature and of course gives you no dynamic
> information. It would also of course contain all the degrees of freedom of
> the water etc so you might not get a good minimum.

I am at Amber just to have dynamics. I have already carried out DFT at high
functional and basis set level, including vibrational analysis and temperature
correction, all in vacuum.
>
> You could try running cluster analysis (Tutorial B3) for your trajectories -
> this would tell you what percentage of your trajectory was spent in what
> state, it would also tell you about interconversions between states - I.e.
> to get from state X to state Y the system always goes through state Z - you
> would likely need longer trajectories than 1000 steps to get good statistics
> though and possibly Replica Exchange although I'm not sure on this.

I'll do that. Thanks. What I did so far, is a useful very long simulated
annealing in vacuum that preserved the structure nicely, affording a huge
variety of reasonable conformers. I.e, barriers of 25 kcal/mol were easily
surmounted. Must say that the near planarity of highly conjugated cyclic
carbocycles is better preserved here that with PM3.

Cheers

francesco pietra
 

>
> All the best
> >Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

       
____________________________________________________________________________________
Pinpoint customers who are looking for what you sell.
http://searchmarketing.yahoo.com/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu