[gmx-users] Question regarding genion

[Justin A. Lemkul]

On 6/6/12 5:38 AM, Matthias Ernst wrote:
> 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

> 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?
>

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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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