[gmx-users] Using genbox to REMOVE solvent
mdaily.work at gmail.com
Fri Aug 19 07:01:50 CEST 2011
And I am happy to report that this method produces a viable starting
On Thu, Aug 18, 2011 at 7:02 PM, Michael Daily <mdaily.work at gmail.com>wrote:
> 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?
>> 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.
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> Michael D. Daily
> Postdoctoral research associate
> Pacific Northwest National Lab (PNNL)
> (formerly Qiang Cui group, University of Wisconsin-Madison)
Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
(formerly Qiang Cui group, University of Wisconsin-Madison)
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