[gmx-users] Question regarding genion

[Matthias Ernst]

Hi,

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
-neutral
[snap]
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

[Justin A. Lemkul]

Post by Matthias Ernst
Hi,
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)?

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

Post by Matthias Ernst
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
genion -s system_in_solvent.tpr -o solventions.gro -p topol_water.top -neutral
[snap]
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?

I have also found that -neutral must always be used in conjunction with -conc.
It would be nice if this were not the case.

-Justin
--
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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