[gmx-users] Re: Question about CCl4 box!

PeiQuan Chen gromacs at 163.com
Sat May 3 14:42:01 CEST 2003

Dear gmx-users:
  Thank you for david's help again.
>I see, you have defined a completely rigid molecule. This is a bit
>tricky. As you see there are 10 constraints, which means that GROMACS
>thinks your molecule has only (5*3 - 10 =3D) 5 degrees of freedom left,
>which is incorrect since each molecule can translate and rotate. The
>temperaturs is computed from (IIRC)
> T =3D (2/3)*Ekin/(kT*Ndf*Nmol)
>which means that your effective temperature is wrong. If you do
>temperature couling you have to scale the reference temperature by 5/6
>or 6/5 (that is left as an exercise for the reader).
>Alternatively you can leave out one of the constraints. You will still
>get the same geometry, since the constraint problem is completely
>determined by 9 inequalities. You can leave out any of the 10
   I have leaver out one of the constraints( 4 5 ).
   Now that I can reproduce the exp data of density and DHvap
   Density: exp.(1.594) cacul.(1.572)
   DHvap:   exp.(32.54kJ/mol ) cacul.( 32.38kJ/mol)

   But I can't still the make the tau_p value more smaller.If I make the value smaller.
The problem is the same as I have report.
   I want to ask how to change the tau_p smaller and the simulation doesn't carsh. 

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	

More information about the gromacs.org_gmx-users mailing list