[gmx-users] Re: gmx-users Digest, Vol 46, Issue 79
sudheer babu
sudheer.pbm07 at gmail.com
Tue Feb 26 03:46:54 CET 2008
Thank you for very much for your invaulable suggestions to Justin and Sona.
On Tue, Feb 26, 2008 at 3:54 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: problem about Pr.mdp (Justin A. Lemkul)
> 2. Pressure Coupling for DPPC Bilayers (Sona Aramyan)
> 3. Harmonic dihedral restraints (Robert Johnson)
> 4. TFE in molecular dynamic (Luisa Calvanese)
> 5. TFE in molecular dynamic (Luisa Calvanese)
> 6. Re: Harmonic dihedral restraints (David Mobley)
> 7. Re: Harmonic dihedral restraints (Robert Johnson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 25 Feb 2008 06:13:49 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] problem about Pr.mdp
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1203938029.47c2a2ed31e04 at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Quoting sudheer babu <sudheer.pbm07 at gmail.com>:
>
> > Thanks Mr.Mark for your reply,
> > I am not getting any error, but after Position restrain step, when I see
> the
> > structure of *pr_protein_popc_out.gro in VMD the POPC tails are tilting
> > towards backwards(like pulling). It looks there is gap inbetween two
> > membrane layers, middle part of the protein appears without covering
> POPC
> > moledules, but water and protein structure are fine.
> > Can you pls tell where is the problem ? Is there in any mistake in my *
> > pr.mdp file
> > I am gving description about what steps i have done:
> > 1.The protein simulated in solution for 500ps .
> > 2. Protein inserted into POPC by using "genbox".
> > 3. Steepest gradient energy minimisation for "protein embedded in POPC
> > system" , here strucure is fine
> > 4. Postion restrain for same system
> > - For Protein, POPC and Water force constant -10000 I have used.
> >
> > I am mentioning my *pr.mdp file
> > title = popc restrained
> > define = -DPOSRES -DPOSRES_LIPID -DPOSRES_WATER
>
> Try just restraining the protein, otherwise I don't suspect you're
> accomplishing
> much by restraining every component of your system! That's probably not
> the
> problem, however. See below.
>
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 10000 ; total 50 ps.
> > nstcomm = 1
> > nstxout = 50
> > nstvout = 1000
> > nstfout = 0
> > nstlog = 10
> > nstenergy = 10
> > nstlist = 10
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw = 1.4
> > pbc = xyz
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = Berendsen
> > tc-grps = POPC Protein SOL_Cl
> > tau_t = 0.1 0.1 0.1
> > ref_t = 310 310 310
> > ; Anisotropic pressure coupling is now on
> > Pcoupl = berendsen
> > pcoupltype = anisotropic
> > tau_p = 1.0 1.0 1.0 1.0 1.0
> 1.0
> > compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
> > ref_p = 1.0 1.0 1.0 1.0 1.0
> > 1.0
>
> If I remember the usage of anisotropic pressure coupling correctly, this
> might
> be the source of your problem. You are applying 1.0 bar of pressure in
> the
> diagonal directions, which I'm guessing is the source of the distortion.
> Try
> ref_p = 1.0 1.0 1.0 0 0 0
>
> -Justin
>
> > ; Energy monitoring
> > energygrps = POPC Protein SOL_Cl
> > ; Generate velocites is on at 300 K.
> > gen_vel = yes
> > gen_temp = 310
> > gen_seed = 173529
> >
> > Thanks in advance.
> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 25 Feb 2008 04:49:03 -0800 (PST)
> From: Sona Aramyan <sona_aramyan at yahoo.com>
> Subject: [gmx-users] Pressure Coupling for DPPC Bilayers
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <478608.8855.qm at web53307.mail.re2.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hello,
>
> Would the following be a reasonable way to implement
> anisotropic pressure coupling, for a 128 DPPC /3655
> water bilayer with an aminoacid on it:
>
> ; Pressure coupling is on
> Pcoupl = parrinello-rahman
> pcoupltype = anisotropic
> tau_p = 1.0 1.0 1.0 0 0 0
> compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
> ref_p = 1.0 1.0 1.0 0 0 0
>
>
> Beforehand thank you very very much.
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Mon, 25 Feb 2008 13:10:00 -0500
> From: "Robert Johnson" <bobjohnson1981 at gmail.com>
> Subject: [gmx-users] Harmonic dihedral restraints
> To: "Gromacs Mailing List" <gmx-users at gromacs.org>
> Message-ID:
> <b302c1a40802251010r2633b4deifb20b92dcb65e57e at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello everyone,
> I am trying to calculate the absolute free energy of binding between a
> DNA base and a nanotube. To do this, I am first calculating the free
> energy associated with restraining the base in the correct binding
> geometry in accordance with Boresch et. al. J. Phs. Chem. B., 107,
> 2003. In this paper, all restraints (1 distance, 2 angles, 3
> dihedrals) are assumed to be harmonic. In Gromacs, there already
> exists a harmonic distance restraint. Technically, the angle restraint
> (Equation 4.67 in the manual) is not harmonic. However, for small
> angle displacements it can be approximated as harmonic, so that's not
> a problem either.
>
> However, there is no harmonic dihedral restraint. A reasonable
> solution would be to use an improper dihedral (Equation 4. 59 in the
> manual) for the restraint. Is this alright, or are there any problems
> that could arise from using this? To my knowledge, exclusions are
> defined by bonds. Thus, I don't think I have to worry about the
> improper dihedral affecting the exclusions. Is this correct?
>
> Thanks,
> Bob
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 25 Feb 2008 20:29:46 +0100
> From: Luisa Calvanese <luisacalvanese at hotmail.com>
> Subject: [gmx-users] TFE in molecular dynamic
> To: <gmx-users at gromacs.org>, gmx-users-request
> <gmx-users-request at gromacs.org>
> Message-ID: <BAY131-W14F9C3FFF218C814CAE6DBC9180 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> How become part TFE molecules in a calculation of molecular dynamics?
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> Message: 5
> Date: Mon, 25 Feb 2008 20:29:39 +0100
> From: Luisa Calvanese <luisacalvanese at hotmail.com>
> Subject: [gmx-users] TFE in molecular dynamic
> To: <gmx-users at gromacs.org>, gmx-users-request
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> How become part TFE molecules in a calculation of molecular dynamics?
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> Message: 6
> Date: Mon, 25 Feb 2008 11:47:18 -0800
> From: "David Mobley" <dmobley at gmail.com>
> Subject: Re: [gmx-users] Harmonic dihedral restraints
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <bc2c99750802251147j588e940j23f8a739723f6b52 at mail.gmail.com>
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>
> Robert,
>
> I am not sure which manual you are looking at, but in the GROMACS 3.3
> manual, equation 4.70 gives the dihedral restraint as harmonic.
>
> David
>
>
> On Mon, Feb 25, 2008 at 10:10 AM, Robert Johnson
> <bobjohnson1981 at gmail.com> wrote:
> > Hello everyone,
> > I am trying to calculate the absolute free energy of binding between a
> > DNA base and a nanotube. To do this, I am first calculating the free
> > energy associated with restraining the base in the correct binding
> > geometry in accordance with Boresch et. al. J. Phs. Chem. B., 107,
> > 2003. In this paper, all restraints (1 distance, 2 angles, 3
> > dihedrals) are assumed to be harmonic. In Gromacs, there already
> > exists a harmonic distance restraint. Technically, the angle restraint
> > (Equation 4.67 in the manual) is not harmonic. However, for small
> > angle displacements it can be approximated as harmonic, so that's not
> > a problem either.
> >
> > However, there is no harmonic dihedral restraint. A reasonable
> > solution would be to use an improper dihedral (Equation 4. 59 in the
> > manual) for the restraint. Is this alright, or are there any problems
> > that could arise from using this? To my knowledge, exclusions are
> > defined by bonds. Thus, I don't think I have to worry about the
> > improper dihedral affecting the exclusions. Is this correct?
> >
> > Thanks,
> > Bob
> > _______________________________________________
> > 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!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 25 Feb 2008 17:24:33 -0500
> From: "Robert Johnson" <bobjohnson1981 at gmail.com>
> Subject: Re: [gmx-users] Harmonic dihedral restraints
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <b302c1a40802251424x1cb4745eg693ac4f37da4d498 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Well, the potential is of the form V=k(x1-x2)^2, but I don't see how
> it's harmonic. What you would want is the x1 and x2 to refer to
> dihedral angles. However, the potential in equation 4.70 has this
> weird phi-phi_0 MOD 2pi term and this delta_phi parameter. It's just
> not obvious to me how equation 4.70 can be expanded or rearranged to
> look like a harmonic potential in the dihedral angles. Am I just not
> seeing something correctly?
> Bob
>
>
> On Mon, Feb 25, 2008 at 2:47 PM, David Mobley <dmobley at gmail.com> wrote:
> > Robert,
> >
> > I am not sure which manual you are looking at, but in the GROMACS 3.3
> > manual, equation 4.70 gives the dihedral restraint as harmonic.
> >
> > David
> >
> >
> >
> >
> > On Mon, Feb 25, 2008 at 10:10 AM, Robert Johnson
> > <bobjohnson1981 at gmail.com> wrote:
> > > Hello everyone,
> > > I am trying to calculate the absolute free energy of binding between
> a
> > > DNA base and a nanotube. To do this, I am first calculating the free
> > > energy associated with restraining the base in the correct binding
> > > geometry in accordance with Boresch et. al. J. Phs. Chem. B., 107,
> > > 2003. In this paper, all restraints (1 distance, 2 angles, 3
> > > dihedrals) are assumed to be harmonic. In Gromacs, there already
> > > exists a harmonic distance restraint. Technically, the angle
> restraint
> > > (Equation 4.67 in the manual) is not harmonic. However, for small
> > > angle displacements it can be approximated as harmonic, so that's
> not
> > > a problem either.
> > >
> > > However, there is no harmonic dihedral restraint. A reasonable
> > > solution would be to use an improper dihedral (Equation 4. 59 in the
> > > manual) for the restraint. Is this alright, or are there any
> problems
> > > that could arise from using this? To my knowledge, exclusions are
> > > defined by bonds. Thus, I don't think I have to worry about the
> > > improper dihedral affecting the exclusions. Is this correct?
> > >
> > > Thanks,
> > > Bob
> > > _______________________________________________
> > > 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!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > _______________________________________________
> > 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!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
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>
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> End of gmx-users Digest, Vol 46, Issue 79
> *****************************************
>
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