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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of dpandit.brandeis.edu
> Sent: Thursday, May 29, 2008 12:18 PM
> To: amber.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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Received on Sun Jun 01 2008 - 06:07:38 PDT
