AW: Require Suggestion

From: Norman Geist (
Date: Wed Feb 19 2014 - 01:42:09 CST

Please use VMDs "Namd Plot" plugin to get a graph of the TOTAL energy of the
minimization. Zoom in widely and you might notice that 200 steps of
minimization for such a large system is a joke.


Norman Geist.


Von: [] Im Auftrag
von amit banerjee
Gesendet: Mittwoch, 19. Februar 2014 06:40
Betreff: namd-l: Require Suggestion


Dear All,
I am trying to do a simulation of a protein which is large and highly
complex in structure with 3 different domains and each domain contains
complex beta structure.

The longtime goal is to perform SMD simulation with respect to specific
structural points and find the unfolding pattern of such regions.

I tried for an initial simulation in water sphere and planned to move for
water box followed by SMD.

Unfortunately (or fortunately) the initial simulation failed with the error
notice with Rattle algorithm constraint failure for several atoms.

ERROR: Constraint failure in RATTLE algorithm for atom XXXXX!

ERROR: Constraint failure; simulation has become unstable.

The configuration script (and the detailed log file) is attached with this

The minimization step used is 200 and run is used for 1ns (500000).

Alternatively I have tried (after following the NAMD mailing list) with
changing the timestep and cut off values in integrator parameter (from 2 to
1 femtosecond).

The plausible reason for the simulation failure may be due to:

1. Over minimization of the structure during loop refinement (What
Check results also hinted that for the structure)

2. Structural integrity might be getting disturbed due to lower
packing quality of the structure.

My questions in this regard:

1. Can I use the native structure obtained before loop minimization?

2. What are the things I should change in the configuration file?

(I have doubt about the parameter settings I have used here, as most of them
are kept default as per the tutorials.)


Best regards,


CSIR-Indian Institute of Chemical Technology,

Hyderabad,AP, India


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