[gmx-users] how to set up a rigid system

[Yang Ye]

Hi,

Constraints could be in the form of bond or direct constraints (often, in
Gromacs, bonds are treated as constraints). As shown in
http://www.gromacs.org/documentation/reference/online/top.html, you may
write top file as following:

;
;	Example topology file
;
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0

; The force field files to be included

#include "rt41c5.itp"	

[ moleculetype ]
; name  nrexcl
ABC         3

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr  charge
     1       A       1     ABC      C1       1	 0.683	
     2       B       1     ABC      O2       1	-0.683
     3       C       1     ABC      N3       2	-0.622

[ bonds ]
;  ai    aj funct           c0           c1
    1     2     1 1.000000e-01 0.1
    2     3     1 1.000000e-01 0.1
    1     3     1 1.000000e-01 0.1


c0 is the distance in nm. for c1, put a relative large value to make it
stiff.

Yang Ye

On Tue, Dec 9, 2008 at 8:56 AM, Xin Liu <yjqqliu at 163.com> wrote:

> Yang Ye
>
>  I can understand I need to put (3n-6) constraints to the system, but I
> don't know how to describe the constraints in the .itp file. Can you give me
> a example for the case.
> Thank you very much!
> --------------
> Xin Liu
> 2008-12-09
>
>
>


-- 
Regards,
Yang Ye
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