[gmx-users] Genbox - Removal of Unwanted Waters

[David van der Spoel]

Arneh Babakhani wrote:
> Thanks for the input.  Is there a way to restrict the water from a 
> certain space (in other words, to confine it a certain location)?
just the shell option, otherwise no.

genbox -h

> 
> Thanks,
> 
> Arneh
> 
> David van der Spoel wrote:
>> Arneh Babakhani wrote:
>>> Hello all,
>>>
>>> How do you remove unwanted waters (or how do you prevent genbox from 
>>> placing unwanted waters) after you solvate by genbox?
>>>
>>> This problem was posted once before,
>>> http://www.gromacs.org/pipermail/gmx-users/2005-December/018997.html
>>>
>>> but it doesn't seem like it was resolved. Is there an easy way to do 
>>> this (aside from going into the .gro file and manually deleting the 
>>> unwanted waters!)
>>>
>>
>> genbox 3.3.1 has an option to set the maximum number of waters.
>>
>>> Thanks,
>>>
>>> Arneh
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please don't post (un)subscribe requests to the list. Use the www 
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++