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)
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