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 <[EMAIL PROTECTED]> 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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