From: yingxiong (yxiong_at_mail.ccnu.edu.cn)
Date: Mon Mar 08 2004 - 03:55:35 CST
Dear sir,
If I want to fix some non-hydrogen atom during minimization,
I see in the user guide the following information, but it didn't tell me the detailed steps.
Could you please tell me how I should set in configuration?
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6.1.2 Fixed atoms parameters
Atoms may be held xed during a simulation. NAMD avoids calculating most interactions in which
all a ected atoms are xed unless fixedAtomsForces is speci ed.
fixedAtoms < are there xed atoms? >
Acceptable Values: on or off
Default Value: off
Description: Speci es whether or not xed atoms are present.
fixedAtomsForces < are forces between xed atoms calculated? >
Acceptable Values: on or off
Default Value: off
Description: Speci es whether or not forces between xed atoms are calculated. This
option is required for constant pressure or to turn xed atoms o in the middle of a simulation.
fixedAtomsFile < PDB le containing xed atom parameters >
Acceptable Values: UNIX lename
Default Value: coordinates
Description: PDB le to use for the xed atom ags for each atom. If this parameter is
not speci ed, then the PDB le speci ed by coordinates is used.
fixedAtomsCol < column of PDB containing xed atom parameters >
Acceptable Values: X, Y, Z, O, or B
yingxiong
yxiong_at_mail.ccnu.edu.cn
2004-03-08
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