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,
Carsten
Message: 1
Date: 2 Sep 2008 04:47:49 -0000
From: "minnale " <[EMAIL PROTECTED]>
Subject: [gmx-users] Potential energy of POPC
To: "gmx-users1" <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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
PWM
Linnestr. 5
D-04103 Leipzig
Germany
tel +49 341 9732573
fax +49 341 9732479
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