AMBER Archive (2007)

Subject: RE: AMBER: some questions about minimization and MD of DNA duplex with sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Feb 02 2007 - 11:23:02 CST

Hi Wendy,
 
This is a tough one since strictly the structure of the DNA is a function of
the energy of both the DNA itself and the solvent, which reorganises to
accommodate the DNA. For this reason you should probably consider the lowest
overall system energy solvent and DNA combined. However, I suspect that due
to the presence of the solvent the fluctuations in energy will be huge and
you will likely have no structure that is clearly the lowest in energy. For
this reason you may find cluster analysis more useful here. You will be able
to find regions of the trajectory corresponding to different clusters and
then you can average over this region and compare it to the average over
other regions.
 
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 <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.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Chengwen Chen
Sent: Thursday, February 01, 2007 21:40
To: amber_at_scripps.edu
Subject: Re: AMBER: some questions about minimization and MD of DNA duplex
with sander

Dear Ross,
 
I really learn a lot from your reply, thank you very much.
 
Another question is about the structure with the lowest potential energy.
Since my simulation is in explicit solvent, the potential energy from the MD
output file should stand for the energy of the whole sysem including couter
ions and water box . Can it means the DNA duplex is in it's lowest energy?
 
Wendy
 

 
On 2/1/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:

Dear Wendy

 

1. Minimiztion steps:
Before the MD simulation, 7000 steps (2000 for minimizing water box, 5000
for whole system) of minimization is applied. The RMS value of last step is
1.5584E-01. Is it enough? Should I further minimize the system when RMS is
less than 1.0E-03, or even 1.0E-04?
 
This is reasonable for starting MD from. The only reason for doing
minimization before MD is to remove any bad contacts that exist in the
experimental structure and also clashes from adding protons and water
molecules. The main aim is just to remove the largest forces so you should
be good here. If the Md runs fine then don't worry about it. Obviously if
you wanted to do normal mode analysis then you would need a much better
minimum.
 
As an aside you may find it more useful to look at the GMAX value rather
than the just the RMS force value when minimizing since this shows you the
largest force. Compare the GMAX value on step 1 and step 5000 of your
minimization and you should find that it has dropped a lot.

 
2. Analysis of md result:
I noticed that average structure of the overall simulation may not be
reasonable for comparison. Can I take the conformation with lowest energy as
"simulated structure"?
Some published papers provided a analysing method: use CARNAL module of
amber to determine average structures for different conformational families.
But I can't find "carnal" at AMBER9, not even the manual mention this. Is
"CARNAL" avaliable in AMBER9? If not, is there any other module can be used
instead?
 
Average structures are really not very useful in themselves. E.g. consider a
rotating methyl group the average position of those atoms is with the
protons all on top of each other along the axis of rotation. Using the
lowest energy simulated structure is perfectly reasonable. You might also
want to consider carrying out cluster analysis on the system. This will
allow you to essentially bin structures into different families. This can
often be quite useful as for example it might show you that to get from one
structure to another the system always has to go through the same
intermediate structure first. It will also give you an idea of the lifetime
of each structure class. It can be fairly subjective due to how big the
clusters are that you pick etc but I think that using it as a guide as to
what to look for is reasonable. An example of how to do this is in Tutorial
B3: http://amber.scripps.edu/tutorials/basic/tutorial3/index.htm

 

4. minimization of average strucuture:
Even I get the average structures for different conformational families, the
minimization of average strucures is still needed. So the question of
minimization steps still exits. I reviewed the reply of similar questions at
AMBER maillist, most recommend a small number of minimiztion steps. But I am
confused. Why not minimize the system to meet converge critia, like RMS=
1.0E-03, or 1.0E-04?
 
It depends on what you want to look at. If you are just interested in the
structure then minimising so much probably won't gain you anything.
Similarly at 10-3 RMS force the energy is probably converged to something
like 6 decimal places so do really need the energy that good? If you want to
try it yourself try minimising to an RMS of 10^-1. Save the structure and
energy and then minimize further until you get to 10^-4 - then compare the
energies and structures. Now if you interested in second derivatives then
the argument is very different.
 
I hope this helps.
 
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 <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