[gmx-users] Replacing a molecule with multiple ions

Mark Abraham mark.j.abraham at gmail.com
Sun Jul 6 13:32:09 CEST 2014


Seems like a straightforward task for the scripting language of your choice
- even grep and sed can do a decent job. Get rid of all but two of the DMA
atoms, change them to whatever ions suit you, and make matching changes to
your [molecules] section manually. You may need to reorder to have all your
lithium atoms together, etc. but there should be no need to renumber


On Sun, Jul 6, 2014 at 10:46 AM, Timothy Click <tclick at nctu.edu.tw> wrote:

> Good afternoon from Taiwan. Does anyone know of or have an effective way
> to replace a solvent molecule with multiple ions? For example, I want to
> replace N,N-dimethylacetamide (DMA) with LiCl ions. genion replaces by 1:1.
> I was hoping to replace 1:2 because DMA is large enough that I would prefer
> to replace the position of two different methyl carbons with either a
> lithium or chloride ion.
> Thanks.
> Cordially,
> 柯明 Timothy H. Click, Ph.D.
> Department of Biological Science and Technology
> Institute of Bioinformatics and Systems Biology
> National Chiao Tung University
> 208 Lab Building 1, 75 Bo-Ai St.
> Dong District, Hsinchu, Taiwan 30062
> (R.O.C.)
> tclick at nctu.edu.tw
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