[gmx-users] restraints on water oxygen atoms

[Justin Lemkul]

On 6/11/13 2:05 AM, Shima Arasteh wrote:
> 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!
>

Please provide a link to an image or images that illustrate what's going on.  If 
molecules are truly overlapping this badly, it sounds like something is very 
wrong with the force field, since such interactions normally cannot arise 
without the system blowing up.

-Justin

-- 
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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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