[gmx-users] restraints on water oxygen atoms

[Shima Arasteh]

These are the all commands to do iteration:
After generating topology 
-    concatenate the protein and bilayer structure files:
    
     #cat dimer-newbox.gro popc-whole.gro > system.gro
      ( Remove unnecessary lines and update the second line of the coordinate file (total number of atoms) accordingly )

-    Use a very strong position-restraining force on protein heavy atoms to ensure that the position of the protein does not change during EM :
     Adding these lines to topology file:
     ; Strong position restraints for InflateGRO
     #include "topol_Protein_A.itp"
     #ifdef POSRE
     #include "strong_posre.itp"
     #endif
     #include "topol_Protein_B.itp"
     #ifdef POSRE
     #include "strong_posre.itp"
     #endif

-    Now, generate this new position restraint file using genrestr:
     #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 100000 100000 100000

-    In the .mdp file used for the minimizations, add a line "define = -DSTRONG_POSRES" to make use of these new position restraints.

-    Scale the lipid positions by a factor of 4:
     #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat

      Updating the .top file and adding POPC 238 to it.
ITERATION
    1.
     Energy minimization with restrained protein
     #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
     #mdrun -deffnm em

  Steepest Descents converged to Fmax < 1000 in 137 steps
  
Steepest Descents converged to Fmax < 100 in 4998 steps
Potential Energy  =  1.1410846e+04
Maximum force     =  9.4570084e+01 on atom 8800
Norm of force     =  3.2672191e+00


     scale down the lipids by a factor of 0.95
     #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat

    2.
    #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr
    # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 area_shrink2.dat

    3.
    # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr
    # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 area_shrink3.dat
  
    .
    .
    .
    .




Then, after 32 iterations, the APL reaches the value of 10% higher than the experimental value. So, I use the last gro file em_shrink32.gro as the initial configuration to solvate and next steps. But when I check the overlaps in  em_shrink32.gro, there are many improper overlaps and acyl penetration to the protein, disgusting! 



Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, June 10, 2013 11:12 PM
Subject: Re: [gmx-users] restraints on water oxygen atoms



On 6/10/13 12:24 PM, Shima Arasteh wrote:
> Would you please tell me which initial deletion radius?
>

It would be easier for you to provide the exact command(s) you're using.  Maybe 
you've posted this information before, but this thread (or at least, related 
topics) has gone on for a very long time and maybe I'm forgetting.

> And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly?
>

A larger shrinking factor, e.g. 0.95 or 0.97, will shrink more slowly.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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