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
--
========================================
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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