[gmx-users] position restrained dynamics & protein size
rituraj purohit
riturajpurohit at gmail.com
Tue Jan 19 11:02:52 CET 2010
Dear friends,
I am working to study dynamic behaviour of a protein molecule, having
3666 atoms. My question is related to position restrained dynamics
step.
What should be the time step in position restrained dynamics ?
This time i am giving 100ps, but i don't know is it sufficient to sock
the water in protein cavities.
Is their any relationship between position restrained dynamics time
step and protein size?
Please advise me.
Regards
Rituraj
On 1/19/10, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: Is there anyone who has tip3p.gro? (Yang Ye)
> 2. dynamic cross correlation map (DCCM) (leila karami)
> 3. CHarmm and popc membrane (P?r Bjelkmar)
> 4. Re: Is there anyone who has tip3p.gro? (XAvier Periole)
> 5. RE: RE: trjconv problem (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 19 Jan 2010 14:28:39 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] Is there anyone who has tip3p.gro?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <1b3c3eeb1001182228m456f561bu64b629f935520663 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> You may find it in gromacs source.
>
> On Tue, Jan 19, 2010 at 2:08 PM, xiao shijun <xshijun at gmail.com> wrote:
>
> > Hi there,
> > Recently, I cannot add tip3p water in my system, because GMX
> > cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has
> > tip3p.gro, and could you please give me one copy.
> > highly appreciate!!
> >
> > shijun
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
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>
>
> --
> Regards,
> Yang Ye
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> ------------------------------
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> Message: 2
> Date: Tue, 19 Jan 2010 10:31:50 +0330
> From: leila karami <karami.leila1 at gmail.com>
> Subject: [gmx-users] dynamic cross correlation map (DCCM)
> To: gmx-users at gromacs.org
> Message-ID: <f63182a1001182301u2b2e3682mffe2d06e0467ea at mail.gmail.com>
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>
> Hi
>
> I want to obtain dynamic cross correlation map (DCCM). I used following
> command for obtaining covariance matrix.
>
> g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
> covar.log -xpm covar.xpm.
>
> my system consists protein of 70 aminoacids. I want survey correlated and
> anti-correlated motion between residues.
>
> Is my manner true? If so, which of output files in above give me dynamic
> cross correlation map (DCCM)? otherwise, please guide me.
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>
> Message: 3
> Date: Tue, 19 Jan 2010 08:22:42 +0100
> From: P?r Bjelkmar <bjelkmar at cbr.su.se>
> Subject: [gmx-users] CHarmm and popc membrane
> To: gmx-users at gromacs.org
> Message-ID: <4E67E074-3AE0-4FF4-8B34-F41FA5C7DFA3 at cbr.su.se>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi,
>
> > I still don't see it (see below), is this [no]chargegrp new in the cvs ?
> > I'm pretty sure that you're not referring to [no]lys, etc.
>
>
> Yes, that seems to be the case indeed. I've got it in my 'cvs' installation but not in my 4.0.7.
>
> /Pär
>
> ------------------------------
>
> Message: 4
> Date: Tue, 19 Jan 2010 09:58:18 +0100
> From: XAvier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-users] Is there anyone who has tip3p.gro?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <316B572B-99F3-4447-81CB-551EF2F0AFA0 at rug.nl>
> Content-Type: text/plain; charset="us-ascii"
>
>
> You can use spc216.gro ... they have basically the same structure.
> You could also equilibrate the spc216.gro file with your tip3p setup.
>
> On Jan 19, 2010, at 7:28 AM, Yang Ye wrote:
>
> > You may find it in gromacs source.
> >
> > On Tue, Jan 19, 2010 at 2:08 PM, xiao shijun <xshijun at gmail.com>
> > wrote:
> > Hi there,
> > Recently, I cannot add tip3p water in my system, because
> > GMX cannot find tip3p.gro in GMXLIB. I am wondering is there anyone
> > who has tip3p.gro, and could you please give me one copy.
> > highly appreciate!!
> >
> > shijun
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.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
> >
> >
> >
> > --
> > Regards,
> > Yang Ye
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
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> ------------------------------
>
> Message: 5
> Date: Tue, 19 Jan 2010 10:09:58 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] RE: trjconv problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W5406925DC33C58DF108E468E650 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> I fixed the bug.
>
> But note that this is about residue numbers, not molecules.
> The pdb format can not store molecule numbers.
> The pdb format is very inconvenient, but unfortunately it is the most used format.
>
> Berk
>
> Date: Mon, 18 Jan 2010 16:51:19 -0200
> From: stefhoor at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: trjconv problem
>
>
>
>
>
>
>
> Hi,
>
>
>
> It is not a pdb2gmx feature, but a global one.
>
> pdb2gmx is only affected in the sense that it retains the residue numbers from the input pdb.
>
> I assume those will be different for most lipid pdb files (if you use pdb2gmx for those).
>
> This renumbering is done by any program that needs to output or select global residue numbers.
>
> Currently this is switchable with the env.var. I mentioned.
>
> If you put this env.var. in your GMXRC, you can get things how you want them.
>
> Adding an option to all programs is not a good idea.
>
>
>
> But I am open for any suggestions on this issue.
>
>
>
> There is something I don't get though.
>
> In the problematic output the lipids can not be one single residue, but should be two or more residues.
>
>
>
> Berk
>
>
>
> > Date: Mon, 18 Jan 2010 10:31:19 -0500
>
> > From: jalemkul at vt.edu
>
> > To: gmx-users at gromacs.org
>
> > Subject: Re: [gmx-users] trjconv problem
>
> >
>
> >
>
> > Could renumbering be a switchable feature? For instance, pdb2gmx -[no]renumber,
>
> > with "no" being default? Otherwise, could you provide an example of how to
>
> > properly use the environment variable you posted, since this would seem to
>
> > affect all of us in the membrane protein world quite distinctly (i.e., a
>
> > singly-numbered lipid, as reported, kills many of the programs we have written
>
> > for lipid analysis).
>
> >
>
> > -Justin
>
> >
>
> > Berk Hess wrote:
>
> > > Hi,
>
> > >
>
> > > This is a feature.
>
> > > For a long time users have been complaining that pdb2gmx renumbers the
>
> > > residues in a protein.
>
> > > I have now changed this such that the residue numbers in the pdb are
>
> > > retained.
>
> > > But for for instance solvent you would not like to have this behavior.
>
> > > So I decided to keep numbering single-residue molecules.
>
> > > If you also want you lipids to continue numbering, you'll have to set
>
> > > the env.var. GMX_MAXRESRENUM
>
> > > to the number of residues in a lipid.
>
> > >
>
> > > Berk
>
> > >
>
> > > ------------------------------------------------------------------------
>
> > > Date: Mon, 18 Jan 2010 13:05:42 -0200
>
> > > From: stefhoor at gmail.com
>
> > > To: gmx-users at gromacs.org
>
> > > Subject: [gmx-users] trjconv problem
>
> > >
>
> > > I am trying to use trjconv to extract frames from my protein/membrane
>
> > > system in order to analyse with gdmat. Before using git's latest gromacs
>
> > > version, everything worked just fine. But now, every coordinate file
>
> > > trjconv gives me has the DPPC lipid molecules without numbering. It is
>
> > > like if my membrane was formed of a single DPPC (huge) residue. So
>
> > > instead of generating DPPC residue 1, 2, 3, 4 ....etc, trjconv gives me
>
> > > DPPC residue 1 with 5000 atoms.
>
> > > Some light on the matter would be great.
>
> > > Thanks
>
> > >
>
> I thank you all for the contributions, but the problem is that the command "trjconv" is making funny things and not pdb2gmx. My residues are all numbered correctly. Even my coordinate.gro file that is generated at the end of the simulation has the correct numbering. The problem is specifically with "trjconv".
>
> The output from trjconv comes out like this:
> "...
> 66ASN O 671 3.212 3.554 5.248
> 66ASN HO 672 3.258 3.625 5.302
> 1DPP C33 673 0.623 5.221 1.344
> 1DPP C34 674 0.461 5.360 1.434
>
> 1DPP C35 675 0.697 5.438 1.420
> 1DPP N 676 0.604 5.327 1.444
> 1DPP C32 677 0.607 5.278 1.583
> 1DPP C31 678 0.722 5.193 1.637
> 1DPP O32 679 0.860 5.229 1.645
>
> 1DPP P 680 0.954 5.102 1.677
> 1DPP O33 681 0.882 4.986 1.620
> 1DPP O34 682 1.094 5.137 1.647
> 1DPP O31 683 0.929 5.088 1.836
> 1DPP C3 684 1.003 5.184 1.912
>
> 1DPP C2 685 0.946 5.209 2.052
> 1DPP O21 686 0.988 5.332 2.111
> 1DPP C21 687 0.939 5.454 2.087
> 1DPP O22 688 0.893 5.479 1.976
> 1DPP C22 689 0.952 5.554 2.195
>
> 1DPP C23 690 1.086 5.626 2.185
> 1DPP C24 691 1.132 -0.046 2.310
> 1DPP C25 692 1.029 0.049 2.372
> 1DPP C26 693 1.080 0.108 2.504
> 1DPP C27 694 1.100 0.015 2.624
>
> 1DPP C28 695 1.147 0.089 2.750
> 1DPP C29 696 1.047 0.189 2.809
> 1DPP C210 697 1.127 0.248 2.925
> 1DPP C211 698 1.046 0.363 2.985
> 1DPP C212 699 1.127 0.411 3.105
>
> 1DPP C213 700 1.093 0.323 3.226
> 1DPP C214 701 1.141 0.402 3.348
> 1DPP C215 702 1.107 0.339 3.483
> 1DPP C216 703 1.135 0.428 3.604
> 1DPP C1 704 0.997 5.089 2.132
>
> 1DPP O11 705 0.921 5.069 2.251
> 1DPP C11 706 0.969 4.974 2.332
> 1DPP O12 707 1.070 4.914 2.295
> 1DPP C12 708 0.886 4.938 2.449
> 1DPP C13 709 0.889 4.790 2.488
>
> 1DPP C14 710 0.996 4.756 2.592
> 1DPP C15 711 0.985 4.603 2.597
> 1DPP C16 712 1.098 4.556 2.689
> 1DPP C17 713 1.061 4.414 2.730
> 1DPP C18 714 1.174 4.351 2.813
>
> 1DPP C19 715 1.189 4.364 2.965
> 1DPP C110 716 1.330 4.335 3.017
> 1DPP C111 717 1.367 4.338 3.165
> 1DPP C112 718 1.514 4.304 3.191
> 1DPP C113 719 1.542 4.329 3.339
>
> 1DPP C114 720 1.691 4.329 3.372
> 1DPP C115 721 1.711 4.346 3.523
> 1DPP C116 722 1.861 4.344 3.549
> 1DPP C33 723 1.394 3.827 1.098
> 1DPP C34 724 1.402 3.868 1.324
>
> 1DPP C35 725 1.337 3.651 1.249
> 1DPP N 726 1.324 3.795 1.223
> 1DPP C32 727 1.185 3.841 1.213
> 1DPP C31 728 1.074 3.797 1.309
> 1DPP O32 729 1.100 3.828 1.446
>
> 1DPP P 730 1.029 3.739 1.561
> 1DPP O33 731 0.892 3.693 1.529
> 1DPP O34 732 1.132 3.642 1.606
> 1DPP O31 733 1.020 3.846 1.680
> 1DPP C3 734 1.118 3.824 1.782
>
> 1DPP C2 735 1.123 3.924 1.898
> 1DPP O21 736 1.254 3.939 1.955
> 1DPP C21 737 1.326 4.049 1.942...."
>
> You see that starting from the second nitrogen atom of my DPPC molecules, the residue number should be 68 and not 2. So this is what trjconv is actually giving me. It is renumbering the solvent molecules but it is not recognising different DPPC molecules. Instead it is writing my DPPC membrane as one single huge molecule.
>
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--
--------------------------------------------------------------------------------------------------
RITURAJ PUROHIT
Assistant Professor, Bioinformatics Division
School of Bio-sciences and Technology (SBST)
Vellore Institute of Technology, University
Address: SBST, VIT University, Vellore-632014,Tamilnadu, India.
Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile)
Fax; +91-416-2243092, E-mail: rituraj at vit.ac.in
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