Dear Kavin and Jason,
Regarding the cutoff, yes you are right!
Dear Kavin, the attached link of the tutorial really helps alot!
Thanks for your time!
On Tue, Aug 4, 2015 at 2:55 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 07:30:02 PDT
