[gmx-users] the broken of the molecules

[Itamar Kass]

  Hi,

If I guess you correctly, you probably mean that when you look on your 
results (using VMD) it seems like it broken. If this is the case, you 
are OK, it might seems so but it is not, if you indeed used PBC.

Best,
Itamar

On 6/09/2010 6:25 PM, kecy_wu at sina.com wrote:
>
> Hello, I do the energy minimization of the butylene box , but some 
> butylene molecules are broken after that. The butylene itp file is 
> produced by PRODRG, as follows:
>
> /[ moleculetype ]
> ; Name nrexcl
> BUT 3/
>
> /[ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CH3 1 BUT C9 1 0.0049 15.0350
> 2 CH2 1 BUT C6 1 -0.02442 14.0270
> 3 C 1 BUT C3 1 0.07957 13.0190
> 4 C 1 BUT C2 1 -0.06005 14.0270 /
>
> /[ bonds ]
> ; ai aj fu c0, c1, ...
> 2 1 2 0.155 7150000.0 0.155 7150000.0 ; C6 C9
> 2 3 2 0.153 7150000.0 0.153 7150000.0 ; C6 C3
> 3 4 2 0.135 7150000.0 0.135 7150000.0 ; C3 C2 /
>
> /[ pairs ]
> ; ai aj fu c0, c1, ...
> 1 4 1 ; C9 C2 /
>
> /[ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 2 112.5 520.0 112.5 520.0 ; C9 C6 C3
> 2 3 4 2 125.0 610.0 125.0 610.0 ; C6 C3 C2 /
>
> /[ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 1 2 3 4 1 0.0 1.0 6 0.0 1.0 6 ; dih C9 C6 C3 C2 /
>
> //
>
> Can you show me why the butylene molecules would be broken?
>
> Thank you very much !
>
> //
>

-- 


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
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| Victoria 3800
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|
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