Re: AMBER: the total energy is not converge as the cutoff increase

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) <Stefano.Pieraccini.unimi.it>
Date: Mon, 06 Mar 2006 09:28:52 +0000 (GMT)

Dear Thanyarat,

probably the value of the energy at the first step of minimization may be not very indicative. Did you actually perform the minimization or did it crasch? The energy term which seems to increase more with the 20 A cutoff is the electrostatic one, as it might be expected, as elecrostatic term obeys a slow decaying potential. It woud be useful to know why you preferred not to use PBC, and if you use explicit solvent.

Best regards

Stefano Pieraccini


----- Messaggio Originale -----
Da: thanyarat Udom
Data: Lunedi', Marzo 6, 2006 10:00 am
Oggetto: AMBER: the total energy is not converge as the cutoff increase
A: amber.scripps.edu

> Dear Amber users
> I want to run an energy minimization of
> protein/water/counter ions system. First, I have tested cutoff
> the value of non-bonded. I summarized the output from the first
> step (NSTEP = 1) of energy minimization as follows.
> cut off Total Energy(NSTEP=1) BOND ANGLE DIHED
> VDWAALS EEL
> 10 -145910 2629.283 5045.8942
> 10443.8164 30238.3127 -243907.946
> 12 -262380 2629.283 5045.8942
> 10443.8164 29518.1267 -356388.753
> 15 -302340 2629.283 5045.8942
> 10443.8164 29052.2034 -395395.948
> 18 -260040 2629.283 5045.8942
> 10443.8164 28855.7353 -355521.277
> 20 -571410 2629.283 5045.8942
> 10443.8164 28731.883 -667743.075
>
> Surprisingly, the total energy is not converge as the cutoff
> increase. Particularly, the results at cutoff = 20 look very
> strange. The minimization has not been employed PBC (ntb =0).
> Please help me.
>
> Best Regard
> Thanyarat
> Udommaneethanakit
>
>
>
> ---------------------------------
> Yahoo! Mail
> Bring photos to life! New PhotoMail makes sharing a breeze.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Mar 12 2006 - 06:10:07 PST
Custom Search