[gmx-users] genion

[X.Periole]

I don't think it is a good idea to fix the ion but the way 
to do is by introducing position restrain into the ion.itp
after the definition of Cl. You follow the exemple in a 
automaticaly generated topol.top. and edit a posres.itp

XAvier


On Wed, 2 Mar 2005 10:08:27 -0800
  "Nancy Deng" <jdeng at adrik.bchs.uh.edu> wrote:
> Dear All,
> 
> After ideally generated the Cl- location with the 
>"genion -random...", i started to run energy minimization 
>by 200 steps "sd". I noticed the Cl- move to the protein 
>after few steps sd. One way to solve this probem coming 
>my mind is to fix Cl- during all the simulation ( 
>including later production phase data collection).
> 
> I tried to generate a new topology file, neu.top, for 
>the neutralized system. In addition to the "neu.top", 
>four files so named neu_A.itp, neu_B.itp, posre_A.itp, 
>posre_B.itp were output automatically, A for protein, and 
>B is the Cl- respectively. 
> 
> My question is how to specifically fix Cl- only. I know 
>one line in .mdp file: "define =-DPOSRES"  is generally 
>for position restraint But could anyone please tell me 
>how to specifically fix either A or B, or both ( in my 
>example)??? 
> 
> Any of your suggestion is highly appreciated!!!
> 
> nancy 
> 
> 
>  ----- Original Message ----- 
>  From: Nancy Deng 
>  To: Discussion list for GROMACS users 
>  Sent: Tuesday, March 01, 2005 2:23 PM
>  Subject: Re: [gmx-users] genion
> 
> 
>  I have not get a chance to try yet. But I will 
>definitely keep you updated with my new result very soon.
> 
>  thanks,
> 
>  nancy
>    ----- Original Message ----- 
>    From: Dallas Warren 
>    To: Discussion list for GROMACS users 
>    Sent: Tuesday, March 01, 2005 1:50 PM
>    Subject: Re: [gmx-users] genion
> 
> 
>      Probably genion placed solvent inside the protein, 
>and you used genion without the -random option. In that 
>case it places the ion where the potential is most 
>favorable, which will usually be inside the protein.
> 
>    Has that been fixed?  I haven't tried to use the 
>option for awhile now, as last time I did that was broken 
>and it simply placed all ions along one face of the box.
> 
>    Catch ya,
> 
>    Dr. Dallas Warren
>    Lecturer
>    Department of Pharmaceutical Biology and Pharmacology
>    Victorian College of Pharmacy, Monash University
>    381 Royal Parade, Parkville VIC 3010
>    dallas.warren at vcp.monash.edu.au
>    +61 3 9903 9083
>    --------------------------------------------------------------------------
>    When the only tool you own is a hammer, every problem 
>begins to resemble a nail. 
> 
> 
> 
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