[gmx-users] constraining multiple types of bonds
jalemkul at vt.edu
Fri Nov 9 13:17:34 CET 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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