Dear Adrian,
Thank you for your suggestions. We have simulated DAN in lareg water
box with Na+ ions, and we took care that the DNA is not out of water while
pulling it.
Regarding your second suggestion, we have to work on it.
Thanks again.
kakali.
On Wed, 8 Nov 2006, Adrian Roitberg wrote:
> Kakali Sen wrote:
>> Dear all,
>>
>> We have modified amber code to apply constatnt stretching on DNA by
>> applying an external force.
>> When we apply force in units of kcal/mol/ang we get a force extension curve
>> which looks very similar to the experiment one but the force scale is in
>> between 100-2000 pN rather than between 10-100 pN as in experiment. It is
>> an order higher.
>>
>> On the other hand if we say that force is in pN in amber force array then
>> we have the correct force extension plot (that is between 10 to 100 pN) but
>> then we have problem in getting the correct stretch modulus.It of one
>> order lesser
>> than that obtained experimentally.
>>
>> Thanks for your patience and looking forward for suggestions.
>> Kakali.
>>
>>
> Kakali,
>
> Two or three important things about this:
>
> First, are you sure you have the exact same setup as the experiment ? I mean
> solvent, etc ?
>
> Second, the rate at which you pull is CRUCIAL. I bet that you are pulling
> orders of magnitude faster than experiment. There is not much you can do
> about this, but you should at least do it a number of times frm different
> initial snapshots and different pulling rates to see what the fluctuations
> are.
>
> Third. There is code in amber 9, under the flag "jar" to perform constant
> velocity pullings. We are coding constant force now and might be available
> for the public later on.
>
> Cheers
> Adrian
>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
> ============================================================================
>
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> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt
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Received on Sun Nov 12 2006 - 06:07:07 PST
