[gmx-users] Genion command not working

[Tsjerk Wassenaar]

Hi Deepak,

You have to set the minimal distance between ions lower. Check the help of
genion.

Cheers,

Tsjerk

On Aug 28, 2013 8:04 AM, "Deepak Ojha" <alwaysinthemind at gmail.com> wrote:

Dear Gmxers,

I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and br ions
respectively to the system of pure 108 water molecules.But on running the
command genion I get error message


Processing topology

Back Off! I just backed up topol.top to ./#topol.top.9#
Replacing solvent molecule 12 (atom 36) with NA
Replacing solvent molecule 52 (atom 156) with CL
Replacing solvent molecule 35 (atom 105) with NA
Replacing solvent molecule 17 (atom 51) with CL
Replacing solvent molecule 41 (atom 123) with NA
Replacing solvent molecule 70 (atom 210) with CL
Replacing solvent molecule 44 (atom 132) with NA
Replacing solvent molecule 66 (atom 198) with CL
Replacing solvent molecule 34 (atom 102) with NA
Replacing solvent molecule 29 (atom 87) with CL

-------------------------------------------------------
Program genion, VERSION 4.0.7
Source code file: ../../../../src/tools/gmx_genion.c, line: 85

Fatal error:
No more replaceable solvent!
-------------------------------------------------------




How should I add ions in the system.I have tried doing it but could not get
it please if someone may
point my error.


--
DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others to
live as one wishes to live"
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