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

From: Vlad Cojocaru (
Date: Thu Sep 27 2007 - 10:08:51 CDT

Dear NAMD users,

I forgot to mention that the described error in NAMD come at time step
0, no output being generated apart from the NAMD logfile.


Vlad Cojocaru wrote:

> 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 ?
> Thanks
> Cheers
> vlad

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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