AMBER Archive (2004)

Subject: AMBER: restraint

From: tang kwa (nongtangkwa_at_yahoo.com)
Date: Tue Jan 20 2004 - 10:10:39 CST

Dear All,

I have followed the tutorial MD of DNA in Amber
homepage. The system contains 10 basepairs, 18 Na+ and
water molecules. In equilibration step, the solute was
restrained with 25 kcal/mol/Ang^2 and reduced by 5
kcal/mol/Ang^2 untill no restraint. As I have seen in
input file, the restraint was placed on solute (RES 1
20). My question is that the restraint was placed on
only DNA or both DNA and Na+?
As I understand, it should be placed on residue 1 to
20 which means only DNA. But I have read in some
iteratures that the harmonic restraint was placed on
DNA and Na+ ions, which made me confuse. Or maybe "RES
1 20" means 2 strands of DNA plus 18 ions, or not??
Thank you very much in advance for your explanation.

Sincerely Yours,
TK

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