[gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar
pawan.chinari at gmail.com
Thu Mar 19 11:31:08 CET 2009
Hi Xavier sir,
Thanks for your valuable reply.
How can I refine the non-bonded set-up ?
And where can I specify the time step to 0.0001 ?
I am new to gromacs.
Sorry to ask such questions.
Thanking you,
Pawan
On Thu, Mar 19, 2009 at 2:54 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Doubt regarding membrane protein in POPC bilayer (Pawan Kumar)
> 2. how to get the the force plot after pulling dynamic
> simulation using GMX-3.3 (huifang liu)
> 3. Re: Doubt regarding membrane protein in POPC bilayer
> (XAvier Periole)
> 4. RE: compressibility tensor components, pressure coupling
> anisotropic PR, triclinic systems (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 19 Mar 2009 10:44:44 +0530
> From: Pawan Kumar <pawan.chinari at gmail.com>
> Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer
> To: gmx-users at gromacs.org
> Message-ID:
> <143b0c640903182214n2a603f97q478bfac66f502d3e at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx-users,
>
> Greetings from Pawan.
> I have modelled the structure of a protein using Modeller and then energy
> minimized using gromacs.
> Then I used the popc128a bilayer from Tieleman sir's website for inserting
> the protein.
> I created a bigger bilayer using the genconf command in gromacs.
> I was able to minimize the bigger bilayer and then inserted my protein in
> the bilayer using the genbox command in gromacs.
> I was able to minimize the system.
> But when I tried to do an mdrun for few steps restraining the protein I
> ended with errors like :
> 1) pressure scaling more than 1%
> 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger
> than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation.
> 3) too many lincs warnings.
> 4) Number of grid cells is zero. probably the system and the box collapsed.
>
> I tried to solve these errors by increasing the tau_p value for pressure
> scaling error and higher table-extension value for the 1-4 interaction
> warning in the mdp file but nothing is working out.
> I have given the mdp files at the end for reference.
> Please give me some suggestions as how to continue further.
>
> For energy minimization:
> ------------------------------------
> title = Protein in POPC bilayer
> cpp = /usr/bin/cpp
> define = -DFLEXIBLE
> integrator = steep
> nsteps = 50000
>
> ; Constrain control
> constraints = none
>
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 100
> nstvout = 100
> nstfout = 100
>
> ; nblist update frequency
> nstlist = 10
>
> ; ns algorithm
> ns_type = grid
> rlist = 1
>
> ; Method for doing VdW
> vdw-type = Cut-off
> rvdw = 1
>
> ; Method for doing electrostatics
> coulombtype = Cut-off
> rcoulomb = 1
>
> ; Center of mass control
> nstcomm = 1
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Mode for center of mass motion removal
> comm-mode = Linear
>
> ; Energy minimizing stuff
> emtol = 2250
> emstep = 0.001
>
>
> For mdrun using position restraints:
> ---------------------------------------------------
> title = Protein in POPC
> cpp = /usr/bin/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 10 ps.
> nstcomm = 1
> nstxout = 50
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = Protein Non-Protein
> ; Pressure coupling is not on
> Pcoupl = berendsen
> tau_p = 5.0 5.0
> 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
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> ------------------------------
>
> Message: 2
> Date: Thu, 19 Mar 2009 13:52:09 +0800
> From: huifang liu <huifangliu1985 at gmail.com>
> Subject: [gmx-users] how to get the the force plot after pulling
> dynamic simulation using GMX-3.3
> To: gmx-users at gromacs.org
> Message-ID:
> <e523c6be0903182252i114666bam4bbe591a10a30677 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I am recently doing a SMD. I think i did it very well. But i don't know how
> to get the force plot. Is there some one can give me a suggestion?
> Thank you very much.
>
> Huifang
>
> --
> Huifang Liu (Ph.D. Student)
> School of Pharmacy
> Fudan University
>
> 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
> Shanghai, China, 200032 Cell phone: +86-13764669357
> E-mail: huifangliu1985 at gmail.com Fax: (86-21)54237264
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> ------------------------------
>
> Message: 3
> Date: Thu, 19 Mar 2009 10:06:25 +0100
> From: XAvier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-users] Doubt regarding membrane protein in POPC
> bilayer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <C85DBD34-83CD-4F4C-8A4E-5C4224CB7107 at rug.nl>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> It is a bit difficult to guess what is exactly happening. Your
> starting structure
> seem to be the problem, but your topology could also be partly
> responsible.
>
> One easy thing to do is the decrease your time step to 0.0001 which
> would
> decrease the chances that your system explodes.
>
> Also try to work on refining your non-bonded set-up, it looks like you
> use
> straight and short cut-offs.
>
> XAvier.
>
> On Mar 19, 2009, at 6:14 AM, Pawan Kumar wrote:
>
> > Dear gmx-users,
> >
> > Greetings from Pawan.
> > I have modelled the structure of a protein using Modeller and then
> > energy minimized using gromacs.
> > Then I used the popc128a bilayer from Tieleman sir's website for
> > inserting the protein.
> > I created a bigger bilayer using the genconf command in gromacs.
> > I was able to minimize the bigger bilayer and then inserted my
> > protein in the bilayer using the genbox command in gromacs.
> > I was able to minimize the system.
> > But when I tried to do an mdrun for few steps restraining the
> > protein I ended with errors like :
> > 1) pressure scaling more than 1%
> > 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is
> > larger than the 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation.
> > 3) too many lincs warnings.
> > 4) Number of grid cells is zero. probably the system and the box
> > collapsed.
> >
> > I tried to solve these errors by increasing the tau_p value for
> > pressure scaling error and higher table-extension value for the 1-4
> > interaction warning in the mdp file but nothing is working out.
> > I have given the mdp files at the end for reference.
> > Please give me some suggestions as how to continue further.
> >
> > For energy minimization:
> > ------------------------------------
> > title = Protein in POPC bilayer
> > cpp = /usr/bin/cpp
> > define = -DFLEXIBLE
> > integrator = steep
> > nsteps = 50000
> >
> > ; Constrain control
> > constraints = none
> >
> > ; Output frequency for coords (x), velocities (v) and forces (f)
> > nstxout = 100
> > nstvout = 100
> > nstfout = 100
> >
> > ; nblist update frequency
> > nstlist = 10
> >
> > ; ns algorithm
> > ns_type = grid
> > rlist = 1
> >
> > ; Method for doing VdW
> > vdw-type = Cut-off
> > rvdw = 1
> >
> > ; Method for doing electrostatics
> > coulombtype = Cut-off
> > rcoulomb = 1
> >
> > ; Center of mass control
> > nstcomm = 1
> >
> > ; Periodic boundary conditions
> > pbc = xyz
> >
> > ; Mode for center of mass motion removal
> > comm-mode = Linear
> >
> > ; Energy minimizing stuff
> > emtol = 2250
> > emstep = 0.001
> >
> >
> > For mdrun using position restraints:
> > ---------------------------------------------------
> > title = Protein in POPC
> > cpp = /usr/bin/cpp
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 5000 ; total 10 ps.
> > nstcomm = 1
> > nstxout = 50
> > nstvout = 1000
> > nstfout = 0
> > nstlog = 10
> > nstenergy = 10
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = berendsen
> > tc-grps = Protein Non-Protein
> > tau_t = 0.1 0.1
> > ref_t = 300 300
> > ; Energy monitoring
> > energygrps = Protein Non-Protein
> > ; Pressure coupling is not on
> > Pcoupl = berendsen
> > tau_p = 5.0 5.0
> > 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
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 19 Mar 2009 10:23:27 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] compressibility tensor components, pressure
> coupling anisotropic PR, triclinic systems
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W6C9AF5515358EB563A4798E960 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>
>
> Hi,
>
> If you have a liquid system (no off-diagonal elasticity), you should not
> use full anistropic pressure coupling.
> If you have a solid system (for instance a crystal), you will have an
> elastic shear stress response
> and you can determine and use off-diagonal compressibility values.
>
> You need the compressibility values to set the time scale of the pressure
> coupling.
> The compressibility does not affect any thermodynamic quantity, only the
> dynamics.
> The compressibility always occurs as a product with 1/tau_p.
> If you want to determine them from a simulation, you need a reasonable
> initial guess
> for the compressibility and you can use a large tau_p to be on the safe
> side
> with the actual coupling time.
>
> Berk
>
> Date: Wed, 18 Mar 2009 16:02:38 -0700
> From: lastexile7gr at yahoo.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] compressibility tensor components, pressure coupling
> anisotropic PR, triclinic systems
>
> Hello,
>
> Searching first the gromacs mailing list I could not find an answer to the
> problem I face.
>
> I would like to know the vaules I have to give to the mdp file where it
> asks for compressibility.
> I have to conduct an NPT simulation using barostat Parrinello-Rahman. My
> pressure coupling should be anisotropic. The values I have given up to now
> are:
> tau_p = 1.0
> compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
> ref_p = 1.0 1.0 1.0 0.0 0.0 0.0
>
> when I try to calculate the elastic constants I get reasonable values for
> the diagonal elements, yet not
> good for the off-diagonal. The system I have is a monoclinic one, so
> giving zeros to xy,xz,yz components is not an option.
> An experimental linear compressibility value I have found out is very close
> to the value above, so this is why I think I get good values in the diagonal
> elements.
>
> I have found out many different questions, including one about monoclinic
> systems. In one of them someone was wondering why he had to put as input the
> compressibility values, while he is supposed to calculate them from the
> simulation. As far as the monoclinic system is concerned the question had to
> to with the components in gromacs derived from the linear experimental
> values.. There was no answer to that.
>
> I have tried some different values myself, for the off - diagonal
> components and I get either a crash of my simulation of different results
> for the elastic constants. Is there an algorithm which clearly can point me
> to the right direction on how to derive
> the right values?
>
> Thank you in advance,
> Nikos
>
>
>
> _________________________________________________________________
> What can you do with the new Windows Live? Find out
> http://www.microsoft.com/windows/windowslive/default.aspx
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