On Tue, 2015-08-04 at 10:13 +0000, Abelak, Kavin wrote:
> Dear Alaa,
>
> I think you need to read through the manual (AMBER15, starting chapter
> 18.4) and look closely at what all the flags and parameters mean. I’m
> also fairly new to AMBER and the manual has proved very helpful.
>
> I direct you to
> http://ambermd.org/tutorials/basic/tutorial3/section4.htm where a
> progressive heating script can be found. Although you have to be
> careful as this is for GB implicit solvent and you have to modify your
> parameters accordingly. To answer your specific question, it seems you
> need to put ntx=5 and irest=1.
>
> As for “cut", I don’t think you’re meant to change it between
> sequential runs,
I agree, you should not change the value of the cutoff.
The rest of the advice here looks good as well.
> but maybe someone with more experience can chip in here. And I think
> changing ntpr/ntwx will make analysing the results a bit tricky (also,
> writing every 5000 steps for a 25000 step run will only give you 6
> data-points) unless you are analysing each heating segment
> individually.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 04 2015 - 06:00:04 PDT
