Re: [AMBER] [Amber]Question about softcore

From: yuandandan <yuandandan06.outlook.com>
Date: Fri, 11 Oct 2013 13:48:50 +0000

Hi, dac:
I am glad to receive your reply very much.
 
> However, the MD production was failed once I set the timestep 1.0 fs.
> It seems that the system would fail with timestep 1.0 fs or longer.
 
Yes, it happened for all values of lambda.
If I doní»t use softcore, the MD is all right.
There isní»t any problems with pure MD for V0 structure or V1 structure.
Also, charge appearing or disappearing process is ok.
I think it is the softcore causing the problem.
 
As to my system, it includes three molecules,
two cup-like capsule molecules mouth to mouth and
the linear chain ligand molecule is across the elliptical interspace.
The system is perhaps strain.
Yes, I can run most softcore problems ok. This system is really pronlematic for me.
 
Then, I ran the equilibrium and MD production setting timestep 0.5 fs (MD is ok.).
And, I didní»t get satisfactory results (that is, DV/DL values or relative free energy).
Is timestep 0.5 fs is somewhat improper?
Or, this is not a good system for softcore?
Or, the forcefield (GAFF) is problematic?
 
Best,
dandan
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Received on Fri Oct 11 2013 - 07:00:06 PDT
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