[gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar
pawan.chinari at gmail.com
Tue Apr 7 06:21:00 CEST 2009
Hello Sir,
Can you please tell me how to couple ions with SOL ?
Is there any command in gromacs to do that ?
Thanking you,
Pawan
On Tue, Apr 7, 2009 at 9:44 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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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>>
>> -- ========================================
>>
>> 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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