AMBER: High force constant for MD ???

From: Waqas Nasir <>
Date: Wed, 23 Jul 2008 02:49:46 -0700 (PDT)


Hope every thing is working fine at your side.

Well, I am running minimization and MD studies using sander module of amber version 8 on protein carbohydrate complex. I have to fix the sugar ring so that the conformation remains valid till the end. In minimization, I first tried the force constant of 50 K-Cal/Mol-A**2 which didnt work that well and the ring was distorted, then I jumped to a higher value of 700 (just to make sure that the ring does not move!) which worked out in the end.

Now I am attempting to do the equilibration. Is there any problem if I use the same force constant of 700 in equilibration and MD as well (just on the sugar ring not on the whole complex). I read in the tutorial that its not recommended to use high force constants in MD simulations. Any body with any comments or suggestions?

Thanks alot for reading,
Stay blessed!


PS: Thanks Lachele, for your extensive and worthed help!

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Received on Sun Jul 27 2008 - 06:07:07 PDT
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