[gmx-users] genion

[Nancy Deng]

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
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