[gmx-users] combined ED

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Thu Nov 25 15:40:51 CET 2004

I think it just says that samping of your trajectory is not long enough. Each trajectory just sits in its own local minimum.



Dr. Yuguang Mu
Division of Computational and Structrual Biology
School of Biological Sciences
Nanyang Technological University
Singapore 637820
Tel: 0065-63162885
Mail: ygmu at ntu.edu.sg

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of vincenzo venditti
Sent: 2004年11月25日 22:35
To: gmx-users at gromacs.org
Subject: [gmx-users] combined ED


Dear list,

I've performed two MD on the same pdb file and with the same mdp files,

but when I perform the ED analysis on the concateneted trajectory I find difference along the first eigenvector for the two separate trajectories:


-trajectory 1                                                   -trajectory 2

 averages projection (1st eigenvec)=0.908 nm     averages projection (1st eigenvec)=- 0.906 nm

 rmsf (1st eigenvec) = 0.031 nm                        rmsf (1st eigenvec) = 0.017 nm


I know that two MD simulations on the same sistem difficultly are the same, but what do you think about the extent of the differences?


Thanks in advance,



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