[gmx-users] Removing Water from Final Simulation

[Reid Van Lehn]

FYI you can also take the complement of an existing group with make_ndx
using the ! symbol.

e.g. if water is group 0, you could make a group of everything but water
using:

!0

This might be easier/more foolproof than concatenating all other groups
when generating the appropriate index file as suggested in the previous
email.

Best,
- Reid


On Sun, Jun 2, 2013 at 10:40 PM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

> What group did you select from the list offered when you ran the script?
>  Did it include all of your molecules, minus water?  Or did you just select
> something like "Protein"?
>
> You need to run make_ndx and general a group that contains all of the
> molecules you want.  So you will want to do something like "1 | 2 | 3" when
> running make_ndx  What those numbers are depends on what is contained
> within the gro file you feed it.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> > bounces at gromacs.org] On Behalf Of Parker de Waal
> > Sent: Monday, 3 June 2013 11:53 AM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Removing Water from Final Simulation
> >
> > Thanks Warren for your help, those were exactly the functions I was
> > looking
> > for!
> >
> > However I'm still experiencing a bit of trouble because my simulated
> > protein contained a heme cofactor and it seems to only let me extract
> > one
> > object.
> >
> > Have you had any experience with this?
> >
> > Parker
> > On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren
> > <Dallas.Warren at monash.edu>wrote:
> >
> > > trjconv for trajectories
> > > editconf for coordinate files
> > >
> > > Along with an appropriately generated index file (using make_ndx)
> > which
> > > contains the molecules you want in the output within a single group.
> > >
> > > Catch ya,
> > >
> > > Dr. Dallas Warren
> > > Drug Discovery Biology
> > > Monash Institute of Pharmaceutical Sciences, Monash University
> > > 381 Royal Parade, Parkville VIC 3052
> > > dallas.warren at monash.edu
> > > +61 3 9903 9304
> > > ---------------------------------
> > > When the only tool you own is a hammer, every problem begins to
> > resemble a
> > > nail.
> > >
> > >
> > > > -----Original Message-----
> > > > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> > > > bounces at gromacs.org] On Behalf Of Parker de Waal
> > > > Sent: Monday, 3 June 2013 11:10 AM
> > > > To: gmx-users at gromacs.org
> > > > Subject: [gmx-users] Removing Water from Final Simulation
> > > >
> > > > Hi GMX users!
> > > >
> > > > I just completed my first 30 ns simulation and would to remove all
> > > > water
> > > > molecules from the resulting .gro and trajectory files for the sake
> > of
> > > > my
> > > > HDD.
> > > >
> > > > Does anyone know how to do this?
> > > >
> > > > Cheers,
> > > > Parker
> > > > --
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-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science