AMBER Archive (2008)

Subject: RE: AMBER: NTC and NTF

From: dpandit_at_brandeis.edu
Date: Thu May 29 2008 - 14:39:33 CDT

Thank you, Ross. I am relieved after receiving your reply.

Now, I will focus on analysis of trajectories.

Regards,
Deepa

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> 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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