[gmx-users] How to remove ions from, and from which file in the finished simulation?

[Justin Lemkul]

On 10/19/16 8:05 AM, Marko Sever wrote:
> Hello,
>
> got another question, while I'm finding my way around Gromacs :). I have a
> simulation which I have to continue but I need to remove the ions out of it
> and add just so much ions back that the system will be neutral, because now
> there are too much of them. So I should be working on the .gro file that was
> used for the MD simulation right or maybe also the latest topology file?
>

You need to modify both.  But at this point, you're not "continuing" a 
simulation; you're changing the system and doing a whole new one.

> Can you help me with the commands please?
>

Ions are added with genion.  Manual deletion is done in a text editor.  Refer to 
any basic tutorial for common GROMACS operations, e.g. 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

> Also a bit off topic but where should i look for info regarding steering MD,
> for steering some molecule through a channel?
>

The manual has an extensive section on pulling options.  Also covered in 
tutorials, e.g. 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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