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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon May 16 2011 - 04:20:58 CDT

Hi,

yes, seems possible. In generell it should be a fact, that more precise computing with bigger cutoffs should bring the expected results, as long as they are realistic, bad if they doesn't, good luck.

Best regards

Norman Geist.

-----Urspr√ľngliche 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 10:48
An: NAMD MAILLIST
Betreff: RE: namd-l: deca-Ala simulations with different cutoff produce different results

Hi Norman:

  I have repeated my simulations with the same seed (and single thread running) and it confirms to me that these two simulations leads to different conclusion.
  Maybe, the longer cutoff makes the interactions between the two ends available so the peptide chain twists -- I just guess so.

Jun Zhang
Nankai University
coolrainbow_at_yahoo.cn

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