OK Mark and Justin, thank you for the pointer I will take a look about it A bientot Stephane ------------------------------ Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com ------------------------------
________________________________
De: gmx-users-boun...@gromacs.org de la part de gmx-users-requ...@gromacs.org
Date: jeu. 30/09/2010 13:56
À: gmx-users@gromacs.org
Objet : gmx-users Digest, Vol 77, Issue 201
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Today's Topics:
1. Re: Re: Error : There is no domain decomposition for ....
(Mark Abraham)
2. Re: NAMD simulation in Gromacs (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Thu, 30 Sep 2010 21:48:05 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Re: Error : There is no domain decomposition
for ....
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <fbd7dfad5f039.4ca50...@anu.edu.au>
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----- Original Message -----
From: ABEL Stephane 175950 <stephane.a...@cea.fr>
Date: Thursday, September 30, 2010 21:43
Subject: [gmx-users] Re: Error : There is no domain decomposition for ....
To: gmx-users@gromacs.org
> Mark,
>
> These long range parameters have been used by Bjelkmar et
> al. in their recent paper [1]for simulations of CHARMM ff
> in GROMACS. So I use it !
>
> [1] Bjelkmar, P., P. Larsson, et al. (2010). "Implementation of
> the CHARMM Force Field in GROMACS: Analysis of Protein Stability
> Effects from Correction Maps, Virtual Interaction Sites, and
> Water Models." J. Chem. Theory Comput. 6(2): 459-466.
I'm not questioning any .mdp file settings. However the combination of topology
and initial coordinates contains some kind of bonded interaction between atoms
that are much further apart than you would normally suppose. You should explore
what is going on there.
Mark
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Message: 2
Date: Thu, 30 Sep 2010 21:55:04 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] NAMD simulation in Gromacs
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <fbb29fd25ceae.4ca50...@anu.edu.au>
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----- Original Message -----
From: oguz gurbulak <gurbulako...@yahoo.com>
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users@gromacs.org
-----------------------------------------------------------
| > Dear All,
> I performed a 50 ns md simulation using NAMD and want to continue this
simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation
in Gromacs ? If so, could you please give me the information about this process
?
Not really. You would need to generate a .top in the normal way, and this
process cannot use any topology information that NAMD was using. You could
start the GROMACS simulation from the endpoint of the NAMD simulation, but it
would not be continuous in any sense.
Secondly can I convert NAMD output files into gromacs output files and use
gromacs analysis tools ? Could you please also give me the information about
this issue ?
If you have VMD installed then GROMACS is supposed to be able to link to its
libraries to enable GROMACS tools to read any file format that VMD can read,
which will include all NAMD formats. I'm unaware that anybody has written any
documentation about this, however. That's probably the path of least resistance.
Mark
|
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