AMBER Archive (2009)

Subject: Re: [AMBER] TMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Mar 18 2009 - 05:32:14 CDT

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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