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ELNEDIN(Elastic Network)
- nivedita
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11 years 6 months ago #1196
by nivedita
ELNEDIN(Elastic Network) was created by nivedita
Dear all,
I am trying to do martini + Elastic Network ,i need the value of force constant and r-cut (lower & upper bound).
I run following command
>genrest -f cg.pdb -n index -constr -o constraints
it will generate constraints.itp having distance information but how i select lower or upper bound ?
How i use this value in -elastic -ef value -el value -eu value
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I am trying to do martini + Elastic Network ,i need the value of force constant and r-cut (lower & upper bound).
I run following command
>genrest -f cg.pdb -n index -constr -o constraints
it will generate constraints.itp having distance information but how i select lower or upper bound ?
How i use this value in -elastic -ef value -el value -eu value
Beg for your answer!
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- djurre
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11 years 6 months ago #1199
by djurre
Replied by djurre on topic ELNEDIN(Elastic Network)
If I understand it correct you do not want to use the Elnedyn network, but Martini with an elastic network. Be aware that has not been extensively tested.
Using the Martinize script, you do not need the distance information you get from genrest. This information is generated automatically. You only have to give values for -ef -el and -eu. Since we don't use elastic networks different from Elnedyn a lot, so I don't know what the best values would be. But as a first guess you could use the values used with Elnedyn: -ef 500 -el 0.4 -eu 0.9
But make sure you check you're result for the correct dynamics afterwards!
Using the Martinize script, you do not need the distance information you get from genrest. This information is generated automatically. You only have to give values for -ef -el and -eu. Since we don't use elastic networks different from Elnedyn a lot, so I don't know what the best values would be. But as a first guess you could use the values used with Elnedyn: -ef 500 -el 0.4 -eu 0.9
But make sure you check you're result for the correct dynamics afterwards!
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