[gmx-users] Bond constraints during the equilibration for membrane-protein system

[li lv]

Dear Justin

Thanks greatly for your suggestions. I will try a new series of  EMs and NPT
equilibrations to find whether it will be of effect.

Li

2011/5/14 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> li lv wrote:
>
>> Dear Justin
>>
>>
>> Thanks for your reply. Generally I conduct the simulation following the
>> tutorial on your website. The system contains an integrin alpha2b/beta3
>> transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and
>> solvated in water. The initial membrane-protein system is built with
>> INFLATEGRO. Here is the topology file of the system (not completed):
>>
>> “
>>
>> ; Include forcefield parameters
>>
>> #include "ffG53a6_lipid.itp"
>>
>>
>> ; Include chain topologies
>>
>> #include "topol_A.itp"
>>
>>
>> ; Include Position restraint file
>>
>> #ifdef POSRES
>>
>> #include "posre_A.itp"
>>
>> #endif
>>
>>
>> #include "topol_B.itp"
>>
>>
>> ; Include Position restraint file
>>
>> #ifdef POSRES
>>
>> #include "posre_B.itp"
>>
>> #endif
>>
>>
>> ; Include DPPC chain topology
>>
>> #include "dppc.itp"
>>
>>
>> ; Include water topology
>>
>> #include "spc.itp"
>>
>>
>> #ifdef POSRES_WATER
>>
>> ; Position restraint for each water oxygen
>>
>> [ position_restraints ]
>>
>> ;  i funct       fcx        fcy        fcz
>>
>>   1    1       1000       1000       1000
>>
>> #endif
>>
>>
>> ; Include generic topology for ions
>>
>> #include "ions.itp"
>>
>>
>> [ system ]
>>
>> ; Name
>>
>> Protein in water
>>
>>
>> [ molecules ]
>>
>> ; Compound        #mols
>>
>> Protein_A           1
>>
>> Protein_B           1
>>
>> DPPC 124
>>
>> SOL             17185
>>
>> NA+ 2
>>
>> ”
>>
>>
>> For the details of energy minimization, here is one of the mdp files for
>> energy minimization:
>>
>> “
>>
>> define = -DPOSRES
>>
>> integrator = cg
>>
>> emtol = 500.0
>> emstep = 0.01
>> nstcgsteep = 100
>>
>> nsteps     = 50000
>>
>> nstlist = 1
>> ns_type = grid
>>
>> rlist = 1.2
>> coulombtype = PME
>> rcoulomb = 1.2
>> rvdw = 1.2
>> pbc = xyz
>>
>>
>>
>> freezegrps = Protein-H
>>
>> freezedim = Y Y Y
>> ”
>>
>> As you may notice, I froze the heavy atoms of the protein during the first
>> energy minimization and then in the following the EMs the frozen group was
>> MainChain, C-alpha and none in order. The system finally reached Fmax < 500.
>>
>>
> But do you maintain position restraints?  Restraints during minimization
> serve little use, and they actually are probably preventing some necessary
> structural changes from happening.  I'd suspect that's the reason for your
> instability - you're not minimizing as well as your system requires.
>
> I would also say that there is no point in using both freezegrps and
> position restraints during equilibration, especially NPT, where freezegrps
> actually interfere with proper coordinate scaling.  I would suggest you
> simply use position restraints.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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