Re: FEP: How check equilibration sufficiency? calculate dG?

From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Tue Oct 14 2008 - 02:45:50 CDT

Hi Sebastian,

It's not feasible to compute the absolute value of G for a system of any relevant size - you can only realistically sample over small differences dG on the order of kT. To check convergence you're best off monitoring the cumulative dG average which is calculated as your simulation progresses (the last column in the FEP output file).

Best regards,

Floris

----- Original Message ----
From: Sebastian Stolzenberg <s.stolzenberg_at_gmail.com>
To: Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
Cc: namd-l_at_ks.uiuc.edu
Sent: Tuesday, 14 October, 2008 5:50:43
Subject: namd-l: FEP: How check equilibration sufficiency? calculate dG?

Dear Jerome,

I would like to to check, if for a step lambda1->lamba2, the FEP
equilibration time was sufficiently long.
One criterion I was thinking of was checking convergence of G_1 and G_2
(corresponding to lambda1 and lambda2 respectively)- are these
quantities possible to calculate from the FEP output?
I tried using the energy values, but immediately saw that the numbers
are so large that they will cause overflow in the exponentials of the
partition functions.

Is there a special trick to calculate G_1 or G_2? How did you calculate dG?

Thank you,
Best,
Sebastian

      

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