[gmx-users] genion-Cl

[Nancy Deng]

Dear Xavier,

thank you very much for your response. Then would you mind sharing other
choice to solve the problem of Cl stucking into the protein???

Thanks,

nancy
----- Original Message ----- 
From: "X.Periole" <X.Periole at rug.nl>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, March 02, 2005 12:08 PM
Subject: Re: [gmx-users] genion



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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