You can actually combine targetted MD with WHAM to get a free energy
profile of a system. The reaction coordinate will be, however, not a
physical quantity but the RMS deviation. Check out the following papers:
Noy et al., Theoretical study of large conformational transitions in
DNA: B <-> A conformational change in water and ethanol/water, NAR 35,
3330-3338, 2007.
Banavali and Roux, Free energy landscape of A-DNA to B-DNA conversion in
aqueous solution, JACS 127, 6866-6876, 2005.
You have to be careful if this method will be useful in your system. I do
not know how your system looks like, but if there are conformational
change - within - the molecule, I think targetted MD can be applied. I did
some test calculations on a simple monomer nucleic acid using 2 different
methods: 1) Umbrella sampling + WHAM, 2) Targetted MD + WHAM. Both
predicts the same free energy profiles. Read the papers I gave above, and
see if it will work on your system.
Best regards,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Fri, 8 Apr 2011, Catein Catherine wrote:
>
> Hi Florent,
>
> Could you mind to let me know why it is not suitable for PMF?
>
> Best regards,
>
> Annie
>
>> From: florent.barbault.univ-paris-diderot.fr
>> To: amber.ambermd.org
>> Date: Thu, 7 Apr 2011 19:17:08 +0200
>> Subject: Re: [AMBER] How to apply restraint based on a reference structure?
>>
>> Hi,
>>
>> Targeted Molecular Dynamics can do this. However, I don't think it is
>> suitable for a PMF...
>>
>> Regards
>> Florent
>>
>>
>> On Fri, 8 Apr 2011 01:12:13 +0800
>> Catein Catherine <askamber23.hotmail.com> wrote:
>>>
>>> Dear Sir/Madam,
>>>
>>> How to apply restraint based on a reference structure? but not a
>>> distance nor angle in umbrella sampling? Can it be used for PMF
>>> calculations?
>>>
>>> Best regards,
>>>
>>> Catherine
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> -------------------------------------------------
>> Dr Florent Barbault
>> Maitre de conferences / Assistant professor
>>
>> Universite Paris Diderot
>> Laboratoire ITODYS
>> 15 rue Jean de Baïf, bâtiment Lavoisier
>> 75013 Paris FRANCE
>> http://florentbarbault.wordpress.com/
>> tel : (33) 01-57-27-88-50
>> e-mail : florent.barbault.univ-paris-diderot.fr
>> -------------------------------------------------
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Apr 07 2011 - 11:00:04 PDT
