[gmx-users] Question: How to delete water

[John Whittaker]

To add on to your answer, Justin:

The usage listed in the tutorial instructs you to use the "-nwater" flag
to specify the number of atoms in a water molecule.

The actual script uses "-water" as a flag, without the "n". I noticed this
in a previous version of the script before the usage in the help message
was changed.

Just letting you know that the command on the tutorial page:

(http://www.mdtutorials.com/gmx/membrane_protein/03_solvate.html)

is different than the correct command, but only for that one flag.

- John

>
>
> On 12/10/19 8:24 PM, 변진영 wrote:
>> Dear All,
>> I have gone through the Justin Lemku tutorial for KALP_15 in DPPC. I
>> have reach the last command line in step3 and faced one problem.
>> When I tried  to delete water in my system by running the command line:
>>
>>   Perl water_deletor.pl -in system_solv.gro -out system_solv.fix.gro
>> -ref 033 -middle C50 -nwater 3
>
> Your problem is you are specifying the reference atom as 033
> (zero-three-three) instead of O33 (oh-thre-three, for Oxygen). Hence, no
> reference atoms are found and the bilayer can't be subdivided.
>
> -Justin
>
>> The result message says that
>>
>>   Starting water deletion process…
>>   Option -nwater not set, assuming 3 atoms in the water model.
>>   Defining the middle of the bilayer as z = 3.27570634920635.
>>   ntop = 0
>>   Illegal division by zero at water_deletor.pl line 219.
>>
>> The tutorial said that the -nwater flag defines how many atoms
>> constitute a water molecule and for SPC, there are 3 atoms and so I used
>> the -nwater option in my command line.
>> But the message says “Option -nwater not set, assuming 3 atom in the
>> water model.” How can I set the -nwater option?
>> Any idea on what caused this problem?
>>
>> -Jinyoung
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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