restarting an AMBER simulation (truncated octahedron PBC) in NAMD fails

From: Vlad Cojocaru (
Date: Thu Sep 27 2007 - 08:45:34 CDT

Dear NAMD users,

I have a simulation of 1ns in AMBER (NPT, 300K, 1 atm, PBC with
truncated octahedron box). Before, 200 ps equilibration were performed,
also in AMBER.

I would like to run steered MD in NAMD using the last snapshot of the
AMBER trajectory and input structure for NAMD. So, I followed the
GROMACS manual indication at page 13 to define the cell bases vectors
for a truncated octahedron and I tried to run an SMD simulation.
However, I got the error: "Atoms moving too fast; simulation has become
unstable, "RATTLE constrains failed". Now, the structure is absolutely
fine, being previously equilibrated and simulated with AMBER. So, I
thought that it might be due to the SMD ...

So, I tried to run a standard MD ( I tried NVT, NPT and NVE) from the
same starting structure. All sims failed with the same error as the SMD.

My guess is that this has something to do with the periodic boundary
conditions and the shape of the box...

My question is: Does any of you have successfully started an NAMD
simulation with a structured prepared in AMBER with a truncated
octahedron box? If yes, is there anything I need to do apart from
correctly assigning the cell bases vectors ?



Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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