Dear Sir/Madam,
I am interested to study a reaction coordinate as follows:
X + C-Y ==> X-C-Y ==> X-C + Y
It seems to me that I should define the reaction coordinate as the distances of XtoC and CtoY.
I am think of using PMF with umbrella sampling.
I know how to make two restrainst for umberlla sampling. I also know how to do the 2D-PMF from wham. Is it the only way or best way to study this reaction coordinate?
I am thinking if it is a sensible way to convert the results files to single column before doing WHAM, i.e.
After the 2D-PMF calculation, I should get the result file as follows:
time column 1 column 2
0 2 5
1 2 4.9
......
where the column 1 is the distance between X and C atoms, column 2 is the distance between C to Y.
Borrowing the idea of LCOD to this analysis. I could convert the column 1 and column 2 to a single combined variable, i.e. column 1 - column 2.
By doing this convertion, I may be able to calculate the 1D-PMF against the combined variable using 1D-PMF.
Do you think it is a sensible way to get the work done using umbrella sampling?
Best regards,
Cat
Best regards,
Cat
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Received on Fri Aug 06 2010 - 01:00:04 PDT
