And I am happy to report that this method produces a viable starting structure :)
On Thu, Aug 18, 2011 at 7:02 PM, Michael Daily <mdaily.w...@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.abra...@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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > > > -- > ==================================== > Michael D. Daily > Postdoctoral research associate > Pacific Northwest National Lab (PNNL) > 509-375-4581 > (formerly Qiang Cui group, University of Wisconsin-Madison) > -- ==================================== Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison)
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