Thank you for your advice.
On 2/3/07, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> 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.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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Chengwen Chen
> *Sent:* Thursday, February 01, 2007 21:40
> *To:* amber.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.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 Wed Feb 07 2007 - 06:07:29 PST
