AMBER Archive (2008)

Subject: AMBER: High force constant for MD ???

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Wed Jul 23 2008 - 04:49:46 CDT

Hi,

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!

Regards,
Waqas.

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

      
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