AMBER Archive (2009)

Subject: RE: [AMBER] TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Mar 18 2009 - 06:15:55 CDT

Dear Carlos Simmerling,

I am sorrry,

I could not understand the explanation ,
could you please explain me in detail ,

it will be helpfull fo rme !

regards
balaji
UOM

> Date: Wed, 18 Mar 2009 06:32:14 -0400
> Subject: Re: [AMBER] TMD
> From: carlos.simmerling_at_gmail.com
> To: amber_at_ambermd.org
>
> 1) look at the resrtaint energy. is it high enough to really push it
> all the way given the thermal energy? your force constant is quite
> low.
>
> 2) look at the structure. is it physically possible to convert
> directly to the lower RMSD one from this one? it's not always the
> case, you may have to go up in RMSD first, and that will take energy.
> RMSD is very often a poor reaction coordinate.
>
>
> On Wed, Mar 18, 2009 at 12:58 AM, balaji nagarajan
> <balaji_sethu_at_hotmail.com> wrote:
> >
> > Dear Amber !
> >
> > I have done Targeted molecular dynamics for
> > DNA .
> >
> > In the script i gave the value of
> > tgtmdfrc =0.01 , the Rmsd of the structure is
> > going towards the reference structure but after it reached
> > a particular value it has become stable and its not going towards
> > the rmsd difference of 0
> > the current RMSD value from run is as below
> >
> > 14.517
> > 14.545
> > 14.566
> > 14.554
> > 14.513
> > .
> > .
> > .
> > .
> > .
> >
> >
> > . 5.076
> > 5.069
> > 5.068
> > 5.070
> > 5.064
> > 5.050
> > 5.021
> > 4.997
> > 4.991
> > 4.982
> > 4.980
> > 5.010
> > 5.019
> > 5.020
> > 5.020
> > 5.018
> > 5.009
> > 5.013
> > 5.037
> > 5.051
> > 5.060
> > 5.060
> > 5.060
> >
> >
> > what one has to do for it to make it exactly towards zero .
> >
> > thanks in advance !
> > balaji
> > UOM
> >
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