[gmx-users] RE: Potential energy of POPC (minnale )

Carsten Selle selle at physik.uni-leipzig.de
Tue Sep 2 14:42:48 CEST 2008

Hi minnale,

Regarding the length of your simulation: (in lack of other experience) 
some criteria for assumption of (a kind of) equilibrium in membrane 
simulations are listed in section 2. 6 of C. Kandt et al., Methods 41 
(2007), 475-488. These authors recommend "monitoring the dimensions of 
the simulation box, lipid properies and energies". For more details 
please cf. the paper.  Personally, I think that 5 ns sounds a bit on the 
short side. However, as it is also stated: "Unfortunately, it is 
difficult to suggest exact criteria..."

Hope that helps, best wishes,
> Message: 1
> Date: 2 Sep 2008 04:47:49 -0000
> From: "minnale " <minnale_gnos at rediffmail.com>
> Subject: [gmx-users] Potential energy of POPC
> To: "gmx-users1" <gmx-users at gromacs.org>
> Message-ID: <20080902044749.6491.qmail at f5mail-237-219.rediffmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> Hi all, 
>    I have done popc simulation for 5ns and calculated potential energy of POPC. The values started from -269000 kj/mol reduced to -272000 kj/mol.
> Could you please tell me
> 1.is it require to extend my simulation from 5ns?
> 2. The above mentioned potential energy values whether correct or not?
> Thanks in advance  
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Dr. Carsten Selle
University of Leipzig
Institute for Experimental Physics I
Linnestr. 5
D-04103 Leipzig

tel +49 341 9732573
fax +49 341 9732479

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