AMBER Archive (2009)

Subject: [AMBER] Distance restraint and periodic boundary conditions

From: Cyril Falvo (cfalvo_at_uci.edu)
Date: Tue Aug 18 2009 - 19:58:29 CDT

Dear all,

I am trying to use Amber 9 to perform a restrainted MD simulation with
periodic boundary conditions. I want to restraint the length of hydrogen
bonds in an "infinite" beta-sheet and I am using the option /nmropt=1./
The bonds located inside the periodic box seams to be properly
restrainted. For example I get in the output file the following line /

Rcurr: 2.614 Rcurr-(R2+R3)/2: 0.464 MIN(Rcurr-R2,Rcurr-R3):
0.464/.

My problem is that the bonds across two periodic images are not acting
properly. For example in the output file I have the following line /

Rcurr: 31.444 Rcurr-(R2+R3)/2: 29.294 MIN(Rcurr-R2,Rcurr-R3):
29.294/.

Does that mean that for restrained MD the periodic boundary conditions
are not included ?
Thanks for your help.

Cyril

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