RE: deca-Ala simulations with different cutoff produce different results

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon May 16 2011 - 02:12:40 CDT

Hi Jun,

just from curiosity, have you tried this cases once only or multible tie
with the same result? Couldn't it be happened by accident. Maybe you could
try to initialize both cases with the same random number seed value, to give
the same start impulse.

Best regards

Norman Geist.

-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Jun Zhang
Gesendet: Montag, 16. Mai 2011 07:49
An: NAMD MAILLIST
Betreff: namd-l: deca-Ala simulations with different cutoff produce
different results

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
coolrainbow_at_yahoo.cn

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