deca-Ala simulations with different cutoff produce different results

From: Jun Zhang (
Date: Mon May 16 2011 - 00:48:36 CDT

Hello Everyone:

I am using NAMD to simulate the folding of deca-Ala (Ala10). In literature it states that in vacuum the stable conformation of deca-Ala is alpha-helix, and I want to reproduce this result. I use an extended conformation of deca-Ala as initial configuration, using Langevin dynamics to keep temperature at 300K(gamma=10), without PBC, 0.5fs step.

The issue is that, when I applied the following condition:

cutoff              5.
switching           on
switchdist          4.
pairlistdist        7.

I indeed found that the extended deca-Ala changed to alpha helix configuration. However, when I applied the following condition:

cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

In this case, the deca-Ala contracted to a "twisted" conformation.

So, I am confused about this discrepancy. Does it mean the second set of parameters an unreasonable one? Or other explanations? Any suggestions will be appreciated.

Jun Zhang
Nankai University

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