nmropt doesn't directly affect Rgyr. what nmropt allows you to do is add
additional input to the MD simulation that will (1) change the weights of
various simulation variables (like temperature) or force field components
and (2) introduce restraints to the system. There are many, many options
that are described in the Aber manual.
In your case, if you use nmropt=1 along with a line that varies the TEMP0
thermostate temperature, then the system may become hotter, which may result
in Rgyr changes. If you keep the temperature constant, the Rgyr will
probably be stable. So, there is no direct link between Rgyr and nmropt, and
without knowing much more about what you are trying to to and how much you
know about simulations, thermostats and so on, it's hard to help. If you
don't know much about how simulation methods work, I suggest reading a good
book such as Leach's "Molecular Modeling". Then you can ask here for
specific questions about how to implement these in an Ambre simulation.
You'll also learn a lot by reading the literature and looking for examples
of what other people have done that is very similar to what you want to
accomplish, and then using their methods as a guide for what you might try
to do.
good luck!
On Sat, Sep 5, 2009 at 1:23 AM, Jio M <jiomm.yahoo.com> wrote:
>
>
> Dear Carlos,
>
>
>
> Sir, I donot know much about nmropt option and useage of weight. I just saw
> tutorials (TUTORIAL A5 - SECTION 5---nudge elastic band) for annealing
> treatment, here nmropt =1 is used....
>
>
>
> I am not able to understand why Radius of gyration is not varying when
> nmropt is 0
>
> Can you please give some reference where I can get some nmropt details
> along with how to use weight, (though I have seen the manual)
>
>
>
> Thanks and regards;
>
>
>
> JIomm
>
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] nmropt option
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Friday, September 4, 2009, 6:15 PM
>
> read the start of the mdout file and see what sander says it is doing.
> if you are requesting weight changes, you need nmropt=1 or sander will
> not read it and won't tell you about temperature changes.
>
>
>
> On Fri, Sep 4, 2009 at 2:05 PM, Jio M<jiomm.yahoo.com> wrote:
> > Dear Amber users;
> >
> >
> >
> > anybody please tell use of nmropt . I am doing annealing. I did
> > annealing with both nmropt = 1 and nmropt = 0... and what is
> > requirement to use nmropt option..(as much I know,may be wrong also, it
> > helps in temp0 recognition )
> >
> >
> >
> > hope following information will suffice this discussion:
> >
> >
> >
> > for nmropt = 1, when I plotted Radius of gyration(Rg), the graph shows
> > smooth ups and downs in curve i.e. Rg is varying, as expected, because
> > temp is varied in annealing
> >
> >
> >
> > but for nmropt = 0 Rg donot vary, it decreases
> > initialy and remain same after that.. no ups and down in curve as
> > it should be..
> >
> >
> >
> > thanks and regards,
> >
> > JIomm
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Mon Sep 14 2009 - 11:56:50 PDT
