[gmx-users] InflateGRO and trimer simulation

KM mitomaster at gmail.com
Sun Jan 10 20:06:21 CET 2010

Thank you!
This is what I need, however I keep getting a lot of errors about
uninitialized values. When the script finishes, the membrane is
rescaled, but the protein is untouched in the corner of the new box :(
I'll try to investigate a little bit despite I don't know perl,
however I believe that knowledge of python, C and tcl will help me
understand what's going on.


2010/1/10 patrick fuchs <patrick.fuchs at univ-paris-diderot.fr>:
> Hi,
> the new inflategro with the 'doughnut mode'
> (http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want.
> Ciao,
> Patrick
> 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,
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