[gmx-users] Insert a certain number of water molecules into a nanotube

[Justin A. Lemkul]

toby10222224 at sina.com wrote:
>  Dear all:
> 
>  
> 
>      I am trying to insert a certain number of water molecules into a 
> nanotube with Gromacs-4.0.5.
> 
> When I input the command "genbox -cp tube.gro -ci spc216.gro -nmol 328 
> -try 20 -o",
> 
> I get the following error.
> 
>  
> 
> Program genbox, VERSION 4.0.5
> Source code file: gmx_genbox.c, line: 318
>  
> Fatal error:
> more then one residue in insert molecules
> program terminated
> 
>  
> 
> Should the insert molecules be no more than one residue?
> 

You are using a file (spc216.gro) that contains 216 residues, not one, so 
Gromacs is crashing.

> If it should be, how can I insert 328 water molecules into the tube?
> 
> Are there any other commands in Gromacs that can be used for the same thing?
> 

Two options:

genbox -cp -cs spc216.gro -maxsol 328

or obtain a water.gro that contains 1 water molecule and

genbox -cp -ci water.gro -nmol 328

-Justin

>  
> 
> Thank you in advance!
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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