[gmx-users] Question regarding genion

Matthias Ernst Matthias.Ernst2 at student.kit.edu
Wed Jun 6 11:38:59 CEST 2012


I have to questions regarding genion.

1) Is there a possibility to tell genion in advance which group of 
molecules to replace by ions (for me, solvent is always the choice so I 
want to skript it but I did not find any parameters for this)?

2) I want to neutralize a charged system. Therefore, as I found out, I 
can use the -neutral option. But it seems to me that this option does 
not work if I do not specify a concentration (system has a charge of -52):
genion -s system_in_solvent.tpr -o solventions.gro -p topol_water.top 
Reading file system_in_solvent.tpr, VERSION 4.5.4 (single precision)
Using a coulomb cut-off of 1 nm
No ions to add and no potential to calculate.

If I use genion {parameters as above} -conc 0.0 it also won't add ions 
but if I try e.g. genion {parameters as above} -c 0.0001, it will add 52 
NA and 0 CL ions which corresponds to a neutral system (with -c 0.001, 
it will add 53 NA and 1 CL ions, meaning resulting salt concentration is 
 > 0). I use the amber99sb forcefield.
Is this behaviour desired and do I miss the point of the -neutral option 
not working without specifying a concentration?

Thanks for your help,
Matthias Ernst

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