[gmx-users] Doubt regarding membrane protein in POPC bilayer
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Apr 7 06:14:16 CEST 2009
Pawan Kumar wrote:
> Respected Sir,
>
> Greetings from Pawan.
> Sorry for the inconvenience about the .mdp file.
> The mdp file used for the final run is
> *_
> final.mdp file_*_
>
> _title = Protein in POPC bilayer
> cpp = /usr/bin/cpp
> constraints = all-bonds
> constraint-algorithm= Lincs
> integrator = md
> dt = 0.002
> nsteps = 5000
> nstcomm = 1
> nstxout = 50
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1
> coulombtype = PME
> rcoulomb = 1
> vdw-type = Cut-off
> rvdw = 1
> ; Berendsen temperature coupling is on in two groups
> tcoupl = berendsen
> tc_grps = Protein POPC SOL CL-
> tau_t = 0.1 0.1 0.1 0.1
> ref_t = 300 300 300 300
Don't couple ions seperately. See
http://wiki.gromacs.org/index.php/Thermostats
Mark
> ; Energy monitoring
> energygrps = Protein POPC SOL CL-
> ; Pressure coupling is on
> ;Pcoupl = berendsen
> tau_p = 2.0 2.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> Pcoupl_type = semiisotropic
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
> _*
> mdp file for position restraint mdrun*_
>
> title = Protein in POPC bilayer
> cpp = /usr/bin/cpp
> define = -DPOSRES -DPOSRES_LIPID
> constraints = all-bonds
> constraint-algorithm= Lincs
> integrator = md
> dt = 0.002
> nsteps = 5000
> nstcomm = 1
> nstxout = 50
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1
> coulombtype = PME
> rcoulomb = 1
> vdw-type = Cut-off
> rvdw = 1
> ; Berendsen temperature coupling is on in two groups
> tcoupl = berendsen
> tc_grps = Protein POPC SOL CL-
> tau_t = 0.1 0.1 0.1 0.1
> ref_t = 300 300 300 300
> ; Energy monitoring
> energygrps = Protein POPC SOL CL-
> ; Pressure coupling is on
> ;Pcoupl = berendsen
> tau_p = 2.0 2.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> Pcoupl_type = semiisotropic
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
>
> Thanking you,
>
> Yours sincerely,
> Pawan
>
> On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Pawan Kumar wrote:
>
>
> Respected Sir,
>
> Greetings from Pawan.
>
> 1. Were there gaps between the water and lipid headgroups?
> If so,
> the lipids may be pulling towards the solvent. Restrain the
> lipids
> and run an equilibration for a longer time.
>
> Gap was there when I used a value of 0.5 in the vdwradii.dat
> file. The gap reduced as I decreased the value from 0.5 to 0.35
> to the default of 0.15. I tried all the three possibilities.
> When I used the default vdwradii.dat file and made the solvation
> followed by simulation runs the lipids didnt pull apart. But
> there were water molecules on the sides of the bilayer and not
> in the interior.
>
>
>
> This indicates to me that the gaps are causing the problem. Do not
> run simulations with water in or around the lipids; it is not
> realistic. You can clean up such a starting structure, either by
> some clever script like those on the wiki, or by looking at the
> structure, taking note of which water molecules are offending, and
> deleting them manually from the coordinate file.
>
> The other option is to temporarily give genbox a box that is
> slightly smaller in the x-y dimensions, so that it will try to place
> less water around the POPC periphery.
>
>
>
> 2. 5000 steps is far too short to expect any realistic
> behavior for
> lipids. Equilibration can take upwards of 10-20 ns.
>
> As per your suggestion I have made the final mdrun now again
> with 500000 steps. Hopefully this will work.
>
>
> 3. You haven't mentioned the contents of your .mdp file. Maybe
> you're doing something wrong.
>
> I am using the same .mdp file which I posted before. I have just
> removed the restraints.
>
>
> I don't have record of the previous email; as a general guide, post
> the .mdp by default when experiencing weird behavior. That way the
> users on this list won't have to go combing through the archive to
> find it. If you want free help, make it easy to help you :)
>
> -Justin
>
>
> 4. Are you using Gromos/Berger or OPLS/converted Berger for your
> system? There have been so many of these questions from
> different
> users over the last few days that it's hard to keep track.
> If you
> are using OPLS/converted Berger you may have made a mistake in
> translating the C6/C12 parameters.
>
> I am using gromos 96 force field (G43a1) and as per your
> suggestion I have edited the lipid.itp file to remove the part
> containing " lipid-gromos interactions".
>
>
>
> Thanking you,
>
> Yours sincerely,
> Pawan
>
>
>
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>
>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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