[gmx-users] using 'genbox' for adding solvent

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 21 03:38:16 CEST 2009

Amit Choubey wrote:
> Hi everyone,
> I have been trying to insert a fixed no. of water molecules in my 
> system. I first tried the -cp -cs options and could insert some water 
> molecules. But I still need to insert  few more water molecules and for 
> that i tried using the -nmol -ci option. I made a file named 
> "insert.gro" which has a single water molecule with the right volume 
> associated with it. 
> But this option gave a segmentation fault and i am not sure why its 
> doing that? May be there's not enough space for additional water but it 
> should not give a segmentation fault for that reason. Is there something 
> wrong with my idea?

A segmentation fault with this approach generally indicates that the requested 
number of inserted molecules will not fit.

Alternately, you can try -cs spc216.gro -maxsol (your number)

If the second approach also fails, I would think that would be strong evidence 
that what you're trying to do won't work.


> The insert.gro looks like the following
> H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
>   3
>     1SOL     OW    1    .130    .128    .113
>     1SOL    HW1    2    .037    .126    .150
>     1SOL    HW2    3    .131    .089    .021
>    0.31034   0.31034   0.31034
> I also tried various other box (larger) sizes for this but it didnt help. 
> Thank you in advance.
> Amit
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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


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