[gmx-users] Genbox - Removal of Unwanted Waters

David van der Spoel spoel at xray.bmc.uu.se
Mon May 8 19:42:40 CEST 2006


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
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>>
>>
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-- 
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
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