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

[mohammad agha]

Dear Prof.

Thank you very much from your explanation.

Best Regards
Sara



________________________________
 From: XAvier Periole <x.periole at rug.nl>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, December 13, 2011 6:45 PM
Subject: Re: [gmx-users] antifreeze particle in martini coarse-grained
 


You want to keep the conversation in the list so that others may benefit from it.

No. You need to place 10000 W in the box and manually edit the gro file to change the last 1000 into WF but most importantly in the topology file generate two groups one with 9000 W and the other 1000 WF.
Your way may work but the original placement of the WF might be silly. 

Do not separate the two groups in the mdp file for the temperature control. Leave them together.
 

On Dec 13, 2011, at 4:09 PM, mohammad agha wrote:

Dear Prof.
>
>
>Thanks for your reply.
>
>
>Yes, for example if I need 10000 water, then I place 9000 water by genbox from water.gro file and 1000 antifreeze water from antifreezewater.gro that I changed "W" to "WF" in water.gro and I have in topology file:
>
>
>[ molecules ]
>solute   100
>W        9000
>wf       1000
>
>
>Then my way is correct?
>also I have one group for "WF" in .mdp and index.ndx files, is it correct?
>
>
>Best Regards
>Sara    
>
>
>
>
>
>
>
>  
>
>
>________________________________
> From: XAvier Periole <x.periole at rug.nl>
>To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Sent: Tuesday, December 13, 2011 5:34 PM
>Subject: Re: [gmx-users] antifreeze particle in martini coarse-grained
> 
>
>
>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
>
>
>

-- 
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/e289816d/attachment.html>