From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Nov 07 2008 - 14:38:47 CST
The protocol I usually recommend to people is to first use DOWSER (to
place buried waters), then Helmut Grubmuller's SOLVATE
to generate a closely contoured solvent bubble around the solute, and
then use VMD solvate to get the final cube. The main problem with VMD
solvate is its inability to do a good job with matching the biomolecular
surface, which is where DOWSER and Grubmuller SOLVATE excel. There is
now a vmd interface for DOWSER; in principle something similar could be
written for the Grubmuller solvate tool, although people would still
need to download the solvate program itself separately.
Roman Petrenko wrote:
> I think the "solvate" package which is used (i believe) by all
> beginners in namd should be replaced by something more sophisticated,
> because as it was mentioned before there are big cavities between a
> protein and water after the solvation process.
> The solution i use is to solvate a system in twice larger water box
> than it should be. Then i run very short namd simulation without any
> boundary conditions, which allows waters to quickly fill in those gaps
> in protein. Only after that the box is trimmed to the size just to
> cover the protein and PBC is used in a new simulation run.
> Of course, it is not the smartest solution, but having a nice
> solvation function would eliminate all this hustle and would allow one
> to do PBC right away.
> On Fri, Nov 7, 2008 at 1:45 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>> Dave Rogers wrote:
>>> But it would be nice if someone threw in a function call to
>>> reinitialize the patch grid instead of breaking when this happens...
>>> ~ David Rogers
>> That might be helpful in some cases, but frequently this error occurs
>> because someone has a system that is badly undersolvated, or is doing a
>> constant pressure simulation when they should be doing constant volume. I
>> believe the latter case is what is going on here; from Vlad's description it
>> sounds like there's only a single molecule in the simulation box, in which
>> case the box will collapse if a barostat is used. That isn't to say that
>> automatically reinitializing the patch grid wouldn't be a valid option
>> (although the reason that it's very difficult is you have to essentially go
>> through many of the startup phases all over again, at which point you're
>> essentially starting a new run anyway), but the presence of this error
>> frequently means there's something wrong with the input system, so silencing
>> it in all cases would not be a good idea.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:04 CST