AMBER Archive (2008)

Subject: RE: AMBER: NTC and NTF

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 29 2008 - 14:30:28 CDT

Hi Deepa,

It should not affect your results. However, some argue that setting NTF=1 will actually make the shake algorithm converge faster since the proton is nearer to the correct position to begin with. I'm not sure I buy this argument and to honestly have never bothered to test it. Shake time is generally a very small fraction of total time so it isn't worth worrying about.

Short answer NTC=2 with NTF=1 or NTF=2 should be fine in both cases.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of dpandit_at_brandeis.edu
> Sent: Thursday, May 29, 2008 12:18 PM
> To: amber_at_scripps.edu
> Subject: AMBER: NTC and NTF
>
> Hi:
> In my input file I have used ntc = 2 (bonds involving hydrogen are
> constrained), however, I have not used ntf=2 (bond interactions
> involving H-atoms are omitted). After reading the manual I do not
> think it should affect the output of run adversely but I would like to
> know opinion of the community.
>
> Thank you.
> Deepa
>
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