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.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.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.
>
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Received on Sun Feb 04 2007 - 06:07:47 PST
