AMBER Archive (2009)

Subject: [AMBER] reg-TMD

From: balaji nagarajan (
Date: Tue Apr 28 2009 - 10:23:34 CDT

Dear Amber ,

Thank you
Dr. Ccarlos Simmerling
and Shaowen

I have solved my problem , now the Tmd in explicit water in going
good ,

the problem is with the parameter file , it has been corrected

i need another clariffication regarding the
weighting option

I gave a force and after some time the rmsd is not changing its going at a constant value
if i give the greater force i can not view the transition clearly because it moves from one structure to the other in
a rapid manner ,

is there any option to change the weight after some time during the run
like changing both force and the weighting option ,
 TYPE='TGTRMSD', istep1=1, istep2=1000000,
 value1 = 16.00, value2 = 8.00,

TYPE='TGTRMSD', istep1=1000000, istep2=2000000,
 value1 = 8.00, value2 =1.00,


or is there any way to fix this problem .,


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