[gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar
pawan.chinari at gmail.com
Tue Apr 7 05:40:13 CEST 2009
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
; 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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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