[gmx-users] Problem with equilibrated lipid bilayer structure

Thomas Piggot t.piggot at soton.ac.uk
Tue Oct 16 11:34:16 CEST 2012

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.



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,  <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

Dr Thomas Piggot
University of Southampton, UK.

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