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

[David]

On Sat, 2003-05-03 at 03:52, ³ÂÅæÈ« wrote:
> Dear David: 
>   Maybe I haven't make clear of my problem!
>   I have fixed the CCl4 molecules by using constraints section in my ccl4.itp file to fixed my molecules.
>   The following is my ccl4.itp:(The parameters is adapt form OPLS-AA force field).
> 
> [ atomtypes ]
> ;type    mass    charge   ptype          sigma      epsilon
> CCL4     12.01100   0.248       A    3.80000e-01  2.09340e-01
> CLCL4    35.45300  -0.062       A    3.47000e-01  1.11369e+00
> 
> [ moleculetype ]
> ; name  nrexcl
> CCl4	  3
> 
> [ atoms ]
> ;   nr   type   resnr  residu  atom    cgnr    charge
>     1  CCL4      1      CCl4    CT1     1        0.248
>     2  CLCL4     1	   CCl4	Cl2     1       -0.062
>     3  CLCL4     1	   CCl4	Cl3     1       -0.062
>     4  CLCL4     1	   CCl4	Cl4     1       -0.062
>     5  CLCL4     1      CCl4    Cl5     1       -0.062 
>     
> [ constraints ]
> ;  ai    aj funct        b0       
>     1     2     1     0.17690
>     1     3     1     0.17690
>     1     4     1     0.17690
>     1     5     1     0.17690
>     2     3     1     0.2888765
>     2     4     1     0.2888765
>     2     5     1     0.2888765
>     3     4     1     0.2888765
>     3     5     1     0.2888765
>     4     5     1     0.2888765 
> 
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 =) 5 degrees of freedom left,
which is incorrect since each molecule can translate and rotate. The
temperaturs is computed from (IIRC)
 T = (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
constraints... 


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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