AMBER Archive (2004)

Subject: Re: AMBER: Aldo's PMEMD bug

From: aldo jongejan (jongejan_at_few.vu.nl)
Date: Mon Feb 09 2004 - 09:44:39 CST

Hi,

Hereby I apologize to all of you for my stupid mistake (as I already
did to Bob :-) ). I had taken an input file from a Sander7 MD
simulation and tried to use this in PMEMD... but failed to notice the
inconsistency of this approach and the settings of ntb and igb.
For my other PMEMD simulations I had indeed converted my vacuum
systems to PBC conditions.
I got my simulation running now..... Again, I apologize!

aldo

Robert Duke wrote:

> Folks -
> The problem Aldo turned up with PMEMD reading nmr restraints is really not a
> restraints reading problem. Actually, the input specifies a nonperiodic
> simulation (ntb=0) in combination with ewald (igb=0). This combination is
> inconsistent, as ewald simulations require solvated systems with periodic
> boundary conditions. The bug in pmemd 3.1 is that it does not catch the
> ntb=0, and hangs somewhere while dealing with 0 box lengths and 0 box
> angles. Bottom line on this is, if pmemd hangs on you, please be sure you
> are using ntb>0 (pbc). This check has already been added for the amber 8
> release.
> Regards - Bob
>
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--
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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

e-mail: jongejan_at_chem.vu.nl
tlf:    +31 (0)20 4447612
fax:    +31 (0)20 4447610

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