Subject: CCL: Replies to assessing Langevin Dynamics calculations

From: Tim Mitchell-1 <[email-masked]>
Date: 27 Jun 94 16:22:40 ES

Very many thanks to those of you who helped with my query. The replies were as 
follows:

From: arne @ hodgkin.mbi.ucla.edu ("'Arne Elofsson 
([email-masked])'") @ INET 

I had a paper in JMB (1993:233(760-780) last year 
where I adressed some of the general questions.
The conclusion could almost be that the best simulations
are the ones that stay closest to the X-ray structures,
but that might not really apply if you fix some parts
of the structure. You might get some othr ideas from that paper too.

arne

--------------------------------------------
From: chandra @ yorvic.york.ac.uk (Chandra Verma) @ INET 

I remember i came up with this problem a few years ago and of course did not
do much about it - but on talking to some people we gathered that perhaps an
examination of the rms drift/fluctuations of the different regions would be a
good starting point. you could examine the velocities (temperature) of
different regions of the protein to see if it equilibrated well.

--------------------------------------------
From: GKING @ arserrc.gov @ INET 

Hello Tim,

One thing you could analyse is the statistics of the potential energy.
In my molecular dynamics simulations I calculate the mean, median, and
most probable potential energies.  When these three values are close
to one another I'm satisfied that the system is at equilibrium.

There are a couple of other things you could look at such as rms
fluctuations of the atoms or velocity autocorrelation functions, but
these are not useful unless you have similar information from experiment
or other simulations to compare with.

Regards,
Greg

====================================================================
Gregory King                             Internet: [email-masked]
Eastern Reg. Res. Ctr., ARS, USDA           Voice: (1) 215 233 6675
600 East Mermaid Lane                         Fax: (1) 215 233 6559
Philadelphia, PA  19118-2551
====================================================================

--------------------------------------------
From: alex @ mmiris.ab.umd.edu @ INET 

Take a look at the potential energy with respect to time or the RMS
difference with respect to the starting structure.  Both act as a
check to see if the system is still finding lower energy regions of
conformational space or is fluctuating in a stable region.

Alex MacKerell, [email-masked]
School of Pharmacy
University of Maryland at Baltimore
20 North Pine Street
Baltimore, MD  21201
410-706-7442

--------------------------------------------
From: tennant%hau410.uk.sb.com @ sb.com (Mike Tennant) @ INET 

Hi Tim,
 look at the RMS deviations across the run for various subsets of 
atoms eg CA/ backbone/ sidechains/ solvent and make sure these are 
stable. This gives a better indication than energy fluctuations, esp as 
you are doing LD. Also look at the radius of gyration as an indicator of 
structural stability (this is a measure of the packing of the structure). 
To check that your run makes sense, you should calculate some correlation 
functions and compare with literature values in full solvent simulations. 
This will show whether the friction coefficients have been effective in 
reproducing solvent behaviour eg calc various ring flip and atom displacment 
correlation functions. I can find out some papers for comparison if you 
haven't got them already.

  cheers,

   Mike.

--------------------------------------------

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
_/    _____   ____     _/           SmithKline Beecham Pharmaceuticals Ltd  _/
_/   /  ___\\\\ _ \    _/                                    Brockham Park  _/
_/   | |___  \\|_| |   _/ Tim Mitchell, Comp. Chem.             Betchworth  _/
_/   \___  | |  _ <    _/ Phone:  (0)737 36 4535                    Surrey  _/
_/   ____| | | |_| |   _/ Fax:    (0)737 36 4539                   RH3 7AJ  _/
_/   \____/  |____/    _/ E-Mail: [email-masked]         U.K.  _/
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/