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