[gmx-users] Fwd: i want to use water_detetor.pl script

[Mahboobe Sadr]

Yes, I just wanted to try the script, to figure out what's hapenning.. I
tried both N4 and O11.

Sure.I'll do that.
Thank you  in advance

On Fri, Jun 26, 2015 at 3:10 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/25/15 6:12 PM, Mahboobe Sadr wrote:
>
>> I used spc water and the command was :
>>
>>   perl water_deletor.pl -in bilayer.gro -out bilayer_fix.gro -ref N4
>> -middle C50 -water 3 -v yes
>>
>>
> Using N4 as a reference is a bad idea; you don't want to desolvate the
> headgroups.  This will lead to unstable simulations.
>
> Beyond that, I honestly don't know why it's producing weird behavior.  The
> script is really trivial; surely you can debug what's going on even with a
> few simple print statements.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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