[gmx-users] Problem with equilibrated lipid bilayer structure

[Thomas Piggot]

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,  <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.