[gmx-users] InflateGRO and trimer simulation

patrick fuchs patrick.fuchs at univ-paris-diderot.fr
Sun Jan 10 16:27:30 CET 2010

the new inflategro with the 'doughnut mode'
(http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want.


Justin A. Lemkul a écrit :
> On 1/10/10 5:17 AM, KM wrote:
>> Hello Gromacs Users,
>> I would like to run a simulation of a trimer in a DPPC membrane. I
>> really like the elegant solution that inflategro script offers,
>> however I'm afraid I won't be able to use it, because I need to have
>> lipids in a small space between the monomers right in the center of
>> the box and these will certainly get deleted during the whole
>> procedure. I also need to keep the waters that come with the structure
>> of the protein.
>> Do you have any idea how I can elegantly embed my trimer in a
>> membrane, possibly using somehow modified inflategro?
>> Christopher
> I've built multimeric systems with InflateGRO, but with a lot less 
> constraints than you have :)  You can, for instance, run an inflation 
> step with a very minimal scaling factor (like 1.01 or 1.05) and a very 
> small cutoff (7 or so, but you'd have to play around with this) so you 
> essentially delete lipids in place without moving them too much.  I 
> don't know if the necessary lipids between the monomers will be affected.
> As for preserving water molecules, you could probably just extract their 
> coordinates from a suitably-oriented starting structure and paste them 
> into the InflateGRO output.
> None of this requires modifying InflateGRO, but will likely require a 
> lot of trial and error, if it even works, given the very specific nature 
> of what you need.
> -Justin

!!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31
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