problem about cut and cap

From: sxzheng <>
Date: Sun 3 Nov 2002 20:40:25 +0800

Dear all,
I'm equlibrating a protein with solvatecap 25 A ,belly=1, ntb=0 ,ntp=0 ,ntc=ntf=2 and dt=0,002. I found if I do the dynamics the same as the tutorial of streptavidin using cut=9999 and nsnb=999999,the system will be equlibrated in 50 ps for the Etot and T has been equlibrated. While I use cut=9.0 then the Etot of the system will be fluctuant even for a 1ns's dynamics.
1.How to judge the system with cut=9.0 has been equlibrated.

 The gibbs process will be bomb up for the increasing temperature if I use the belly and cap restrained (ivcap=0, natcap=0,fcap=1.5) unless to set ivcap=2.
2.How to do gibbs with cap restrained.
3.Can the result be accepted for the ivcap=2 wile using watercap.

Thank you very much.
Received on Sun Nov 03 2002 - 04:40:25 PST
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