[gmx-users] RE : gmx-users Digest, Vol 77, Issue 201

[ABEL Stephane 175950]

OK Mark and Justin, thank you for the pointer
 
I will take a look about it
 
A bientot
 
Stephane
 
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Stéphane Abel, PhD
CEA Saclay DSV/IBITEC-S/SB2SM
91191 Saclay, FRANCE
website: http://www.st-abel.com
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________________________________

De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
Date: jeu. 30/09/2010 13:56
À: gmx-users at 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)


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Message: 1
Date: Thu, 30 Sep 2010 21:48:05 +1000
From: Mark Abraham <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] Re: Error : There is no domain decomposition
        for ....
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <fbd7dfad5f039.4ca50595 at anu.edu.au>
Content-Type: text/plain; charset="us-ascii"



----- Original Message -----
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Date: Thursday, September 30, 2010 21:43
Subject: [gmx-users] Re: Error : There is no domain decomposition for ....
To: gmx-users at 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.abraham at anu.edu.au>
Subject: Re: [gmx-users] NAMD simulation in Gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <fbb29fd25ceae.4ca50738 at anu.edu.au>
Content-Type: text/plain; charset="us-ascii"



----- Original Message -----
From: oguz gurbulak <gurbulakoguz at yahoo.com>
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users at 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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