Thank you for very much for your invaulable suggestions to Justin and Sona.
On Tue, Feb 26, 2008 at 3:54 AM, <[EMAIL PROTECTED]> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] problem about Pr.mdp > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting sudheer babu <[EMAIL PROTECTED]>: > > > 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 > [EMAIL PROTECTED] | (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 <[EMAIL PROTECTED]> > Subject: [gmx-users] Pressure Coupling for DPPC Bilayers > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > 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. > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > > > ------------------------------ > > Message: 3 > Date: Mon, 25 Feb 2008 13:10:00 -0500 > From: "Robert Johnson" <[EMAIL PROTECTED]> > Subject: [gmx-users] Harmonic dihedral restraints > To: "Gromacs Mailing List" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > 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 <[EMAIL PROTECTED]> > Subject: [gmx-users] TFE in molecular dynamic > To: <gmx-users@gromacs.org>, gmx-users-request > <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > > > How become part TFE molecules in a calculation of molecular dynamics? > _________________________________________________________________ > Scarica GRATIS la versione personalizzata MSN di Internet Explorer 7! > http://optimizedie7.msn.com/default.aspx?mkt=it-it > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080225/7858d6ea/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 25 Feb 2008 20:29:39 +0100 > From: Luisa Calvanese <[EMAIL PROTECTED]> > Subject: [gmx-users] TFE in molecular dynamic > To: <gmx-users@gromacs.org>, gmx-users-request > <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > > > How become part TFE molecules in a calculation of molecular dynamics? > _________________________________________________________________ > Ti piace giocare con le lettere? Prova ABCLive! > http://messengergiochi.it.msn.com/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080225/505d7a60/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 25 Feb 2008 11:47:18 -0800 > From: "David Mobley" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Harmonic dihedral restraints > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 > <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > > 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" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Harmonic dihedral restraints > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > 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 <[EMAIL PROTECTED]> 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 > > <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 46, Issue 79 > ***************************************** >
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php