AMBER Archive (2009)

Subject: Re: [AMBER] nmropt option

From: Jio M (jiomm_at_yahoo.com)
Date: Sat Sep 05 2009 - 00:23:09 CDT

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_at_gmail.com>
Subject: Re: [AMBER] nmropt option
To: "AMBER Mailing List" <amber_at_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_at_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_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber