[gmx-users] Problem with equilibrated lipid bilayer structure

Jernej Zidar jernej.zidar at gmail.com
Tue Oct 16 02:26:57 CEST 2012

Hi Tom,
  Thanks for the detailed reply.

  Could you please suggest the appropriate cut-offs and/or parameters
I should use?


On Mon, Oct 15, 2012 at 5:46 PM,  <gmx-users-request at gromacs.org> wrote:
> Subject: Re: [gmx-users] Problem with equilibrated lipid bilayer
>         structure
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <507BDA00.8060503 at soton.ac.uk>
> 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

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