[gmx-users] Using genbox to REMOVE solvent

Michael Daily mdaily.work at gmail.com
Fri Aug 19 04:02:51 CEST 2011

I tried an experiment similar to yours - after converting the POPE's to
POPC's when I remove all waters that are near the (lipid-emulsified)
nanoparticle based on a radial criterion and then run genbox again, the
total number of waters decreases by about 1100.  Compared to a control case
(ran genbox on the starting structure) that added 1600 waters, this means a
net loss of about 2700 waters.

In any case this is an important discussion for any of you running MARTINI
models - yes it's straightforward to "convert" lipid molecules but the
result can be a terrible starting structure - fortunately the system can be
regenerated from scratch with a new lipid config overnight.

On Wed, Aug 17, 2011 at 11:54 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 18/08/2011 4:32 PM, Michael Daily wrote:
>> Hi all,
>> I am looking for a relatively easy way to make minor modifications to a
>> solvated system in gromacs without having to replace the whole solvent
>> layer.  Specifically, I'm swapping out some molecules (technically, just
>> swapping residue and atom names) in a MARTINI model and I think this causes
>> clashes with the first solvation shell if I increase the size of the
>> headgroup (e.g. POPE -> POPC).  So what I want to do is simply find any
>> solvent molecules that have severe clashes after this modification and
>> remove them - I know genbox checks for overlaps in this way when initially
>> solvating a system, so is it possible to make it check for and remove such
>> overlaps in an EXISTING system?
> No.
> One way to test your hypothesis is to strip the waters from POPC, resolvate
> it with the right atom size, change it to POPE, solvate the
> previously-solvated structure and see if more waters get added. Now they'll
> be in a contiguous lump at the end of the .gro file.
> Mark
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Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
(formerly Qiang Cui group, University of Wisconsin-Madison)
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