AMBER: RE: a request

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 24 Jan 2007 09:57:32 -0800

Hi Santanu,
 
The input format for QMMM with link atoms is identical to QMMM without link
atoms. Sander takes care of all the link atom treatment for you
automatically. The best is if you can send me the calculation you are
running so I can take a look at it. Please send me the mdin, prmtop and
inpcrd files as well as the output file where you are having problems.
 
It would also be useful to know what system (OS, processor etc) you are
running this on, what compilers you used. Is this serial or parallel? And
which bugfixes have been applied to the Amber installation?
 
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 <http://www.rosswalker.co.uk/> | PGP Key
available on request |

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  _____

From: santanu roy [mailto:66.santanu.gmail.com]
Sent: Wednesday, January 24, 2007 01:11
To: Ross Walker
Subject: Re: a request


 
Dear Sir,
               Thank yoy very much for your reply. I have got my answer.
But I am facing problem while silmulating qmmm system.
 
Can you please send me the input formate for qmmm with link atom method.
Neither in the tutorial , nor in the manual the qmmm formate including link
atom is given. I myself tried out, but getting some error like
'aborting' .
 
I will be highly obliged if you kindly respond.
Thanking you,
Santanu


 
On 1/17/07, Ross Walker <ross.rosswalker.co.uk> wrote:

Dear Santanu,
 
I'm not entirely sure I understand your question correctly. However, I
assume you are refering to the first amber tutorial on modelling DNA. Here
we start doing gas phase simulations where we run two simulations, one
without a cutoff and one with. The key point here is that the cutoff
simulation gives a stable system but the no-cutoff simulation does not. Thus
one could make the "wrong" conclusion that the cutoff sim is giving the
correct result. However, these simulations are in a vacuum at 300K. If I
really took a 10mer of DNA and heated it up to 300K in a vacuum it would not
be stable - the two chains would alsmost certainly come apart and the
molecule would decompose. Thus the no-cutoff simulation is probably correct.

 
The important point is that using a cutoff is 'never' a good idea. You can
get away with something liek 16 angstroms or more in an implicit solvent GB
simulation as there is a dielectric screening factor that reduces things by
a factor of 80. However, realisticlly here one should not use a cutoff if
one can afford it computationally. Electrostatic interactions are so long
ranged that you have to go to 30 or 40 angstroms before you get down to
noise.
 
However, with PME doing periodic boundaries the situation is slightly
different. You should probably read up on thePME method from the papers
cited in the Amber manual and make sure you understand the mathematics.
Essentially what you do is take what is a divergent (infinite) sum of pair
wise interactions in real space and cast it into a convergent sum in
reciprocal space. You then use an FFT to calculate the reciprocal space
contribution. You still have a cutoff of say 8 angstroms or so to account
for VDW interactions and also for load balancing issues. This way 8
angstroms worth of electrostatics is done in the direct space sum within the
cutoff while the remainder is done in reciprocal space and adjusted by an
erfc function (error function) to go to zero at the cutoff. In this way PME
gives you effectively infinite electrostatics without requiring you to
calculate infinite pairwise interactions. Hence why you can essentially use
a cutoff with periodic boundaries without problems - as LONG AS YOU ARE
USING PME.
 
I hope this helps explain things. Note if you further questions it is
probably best to post them to the Amber mail reflector - see
http://amber.scripps.edu <http://amber.scripps.edu/> for details on how to
subscribe.
 
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 <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: santanu roy [mailto:66.santanu.gmail.com]
Sent: Friday, January 12, 2007 08:31
To: amber_tutorial_query.rosswalker.co.uk; ross.rosswalker.co.uk
Subject: a request

 

Dear Sir,
                I have gone through almost all of the amber tutorial, and
tested it.

I have some basic questions as the following
1) why we generally take cutoff as 8 to 10 angstrom? in this case we get
actually correct result, why? in case of no cutoff we get
    worst result. why?
is it like VDW interaction, electrostatic interaction get very less value,
so we should ignore those interaction after that cut off?
and in case of no cut off we consider those interactions, is it the reason
for unstable result?

2) does cut off affect on periodic boundary condition?

I am looking forward for your answer.
Regards
Santanu Roy
 






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