[gmx-users] lipase in ccl4 & chcl3

PeiQuan Chen gromacs at 163.com
Wed Jun 11 12:09:01 CEST 2003

Dear gmx-users:

>Since you describe only very little, I can only guess. You may be using
>Lincs to constrain the bond lengths *and* *angles* in CCl4/CHCl3, which
>means you have 5 atoms with 4 bonds (= 4 constraints) and 6 angles (= 6
>constraints), ie 5 atoms + 10 constraints. That is beyond what Lincs was
>designed to handle. If you need angles constrained, use SHAKE in stead.
   When you use SHAKE to constrain the bond lenths and angles in CCl4/CHCl3, you have 
defined a completely rigid molecule. But as David have told me before, you have used 10 constraints, 
which means that GROMACS thinks your molecule has only (5*3-10 = 5 ) degrees of freedom left.
which is incorrect since each molecule can translate and rotate.  The temperature is computed from (IIRC)
            T = (2/3)*Ekin/(kT*Ndf*Nmol)
which means that your effective temperature is wrong.
   If I will do it, I will use constraints section in the top file to implement it. I will use 
any 9 pairs of atomic distance to constraints it, ie using additional bond of appropriate length 
to fix box angle(For example Cl-Cl distance).
   Hope this help!

Sincerely yours
PeiQuan Chen
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	

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