AMBER Archive (2009)

Subject: [AMBER] TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Tue Mar 17 2009 - 23:58:37 CDT

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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