[gmx-users] antifreeze particle in martini coarse-grained

[XAvier Periole]

It was a good idea to ask! You might want to try the MARTINI forum at  
the cgmartini.nl web site, though.

In short the way you did it will probably fill up the box with more  
water or antifreeze particle than necessary ...

As an alternative you may want to simply replace 10% of the existing  
waters into antifreeze particles. You need to change the name in the  
gro files and adapt the topology accordingly. Then an equilibration  
will disperse the WF particle pretty fast.

XAvier.

On Dec 13, 2011, at 2:56 PM, mohammad agha wrote:

> Dear Prof.
>
> I have a doubt about my way to add antifreeze water to my system,  
> also I think my question looks silly but please help me for more  
> certainty.
> I changed "W" to "WF" in water.gro file of water that I downloaded  
> from MARTINI site and named that antifreezewater.gro , and with  
> below command added antifreeze water to my system:
> # genbox -cp -------.gro -cs antifreezewater.gro -o --------.gro - 
> maxsol 1000
> Already I had added water.gro to my system with the same command.
> May I know that I am right or wrong and if I'm wrong please say me  
> the right way?
>
> Thanks
> Best Regards
> Sara
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
>  before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111213/5aac5e7f/attachment.html>