[gmx-users] constraining multiple types of bonds

[Justin Lemkul]

On 11/8/12 11:36 PM, tarak karmakar wrote:
> Thanks Justin
> As you see in the .mdp file I have used SHAKE. So if I want to fix
> some C-C or C-O then what algorithm I have to use ?
>

It still doesn't make sense to me why you want to constrain only a subset of the 
bonds in the system.  Please explain.

> In my topology file I have specified following bonds to be
> constrained. The first two are covalent and the last one is M-L
> non-covalent bond.
>
> [ constraints ]
> ;  index1  index2   funct          length(nm)
>      6062   6063       1        0.11490000000
>      6062   6064       1        0.11490000000
>      6060   4309       1        0.21000000000
> Now while implementing SHAKE it is showing
>

This may be the source of your error.  Without an explanation to the above 
point, it is hard to suggest a fix.  For the metal-ligand interaction, I have 
already suggested two alternative approaches.

> Program mdrun, VERSION 4.5.5
> Source code file: invblock.c, line: 79
>
> Fatal error:
> Double entries in block structure. Item 5247 is in blocks 1371 and 1370
>    Cannot make an unambiguous inverse block.
>
> Please suggest me the exact protocol.

Please answer the above point, which I inquired about previously.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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