Hi Jernej,
You can have a look at our paper linked by both Peter and Sebastien
earlier in this thread, which has a detailed methods section.
Alternatively search in the GROMACS mailing list archives, as this has
been discussed in detail before.
Cheers
Tom
Jernej Zidar wrote:
Hi Tom,
Thanks for the detailed reply.
Could you please suggest the appropriate cut-offs and/or parameters
I should use?
Thanks,
Jernej
On Mon, Oct 15, 2012 at 5:46 PM, <[email protected]> wrote:
Subject: Re: [gmx-users] Problem with equilibrated lipid bilayer
structure
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Hi Jernej,
The CHARMM force field was developed for use with the TIP3P model making
this probably the appropriate choice, even if this model may not perform
the best for simulations of pure water (see
http://pubs.acs.org/doi/abs/10.1021/jz200167q for some more details).
As for some specific GROMACS points with the CHARMM36 lipids. Firstly I
recommend you to use the CHARMM TIP3P variant and secondly you should
also be careful with the cut-off's you choose. I do not think a
dispersion correction would be appropriate and you should also probably
be using some different cut-off's to those you give in you mdp
(typically a switching off of the van der Waals interactions is done
with this force field). Finally you also need to be careful constraining
all bonds (instead of just bonds to hydrogen atoms) with this force
field. We found that we needed to increase the accuracy of the LINCS
settings when constraining all bonds to ensure energy conservation.
Cheers
Tom
--
Dr Thomas Piggot
University of Southampton, UK.
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