[gmx-users] Re: Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole) (XAvier Periole)
XAvier Periole
x.periole at rug.nl
Fri Jul 3 13:29:07 CEST 2009
> I did remove the center of mass motion from my system. But did not
> do it separately for the lipids and solvent. Oh dear ... thats not
> good ... is it ?
Then you should use g_traj to plot the COM of your bilayer and of the
water separately and look at them ...
> Is this just a problem which can be corrected after the simulation,
> or are the simulations now completely useless ?
Unfortunately, no! but you do Martini ... rerunning should not be too
long?
> -MAria
>
> On Fri, Jul 3, 2009 at 12:27 PM, <gmx-users-request at gromacs.org>
> wrote:
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> Today's Topics:
>
> 1. Re: protein covalently bond to ligand (Tsjerk Wassenaar)
> 2. waters in ion channels (Samik Bhattacharya)
> 3. Re: waters in ion channels (Itamar Kass)
> 4. Re: how to center a MARTINI trajectory so that the lipid
> bilayer remains at the center of the box (XAvier Periole)
> (maria goranovic)
> 5. Re: Re: how to center a MARTINI trajectory so that the lipid
> bilayer remains at the center of the box (XAvier Periole)
> (XAvier Periole)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 3 Jul 2009 12:03:48 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] protein covalently bond to ligand
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <8ff898150907030303m6d941470j4317dabe6b8935a0 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi hazizian at razi.tums.ac.ir,
>
> I think it's better to only use PRODRG for the pyridoxal phosphate
> part. Then you can process the rest of the protein as usual,
> preserving the parameters for lysine backbone and side chain. The PLP
> part you can renumber and merge with the protein topology, adding
> bond, angles and dihedrals for the connection. Alternatively you could
> rewrite the PLP topology as a .rtp entry and add the connection in the
> file specbond.dat.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jul 3, 2009 at 9:03 AM, hazizian<hazizian at razi.tums.ac.ir>
> wrote:
> > Hi
> > I want to do MD with a protien with prydoxal phosphate(PLP) which
> attache
> > covalently to one lysine.
> > For this I extract the Toplogy of lysine-PLP from PRODRG server.
> (DRGGMX.ITP
> > and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp.
> > after donig
> > pdb2gmx -f m.pdb -o m1.pdb -water spce with the protein without PLP
> > (m.pdb=protein whitout covalent bond) , I modified the topol.top
> file
> > followig this:
> > 1- add "DRG.itp" under the forcefield section on topol.top
> > 2- add "DRG 1" under the molecule sectin of topol.top
> > also I modifed m1.pdb:
> > cut the related lysine (LYS 360) in the m1.pdb and paste the
> modified lysine-
> > PLP (DRG 360)coordination from DRGPH.PDB.
> > then I do editconf -f m1.pdb and genbox -f m1.pdb successfully,
> but when I
> > want to do grompp the following fatal error appeared:
> > There is no DRG moleculetype.
> > what should I do now?
> > Thanks.
> > --
> > Tehran University of Medical Sciences
> > www.tums.ac.ir
> >
> >
> > --
> > This message has been scanned for viruses and
> > dangerous content by MailScanner, and is
> > believed to be clean.
> >
> > _______________________________________________
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 3 Jul 2009 15:38:42 +0530 (IST)
> From: Samik Bhattacharya <samikbhat at yahoo.co.in>
> Subject: [gmx-users] waters in ion channels
> To: Gromacs <gmx-users at gromacs.org>
> Message-ID: <920957.8244.qm at web95412.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hi i'm simulating a ion channel protein in DPPC membrane. i'm
> following Justin's tutorial for that. and have completed upto the
> solvation step. but right after solvation, i found some water
> molecules in the channel. now i want to delete those molecules. in
> the tutorial it is advised tyo use the keepbyz script to do that..
> but after using that i didn't find any change in the structure.
> watres are still present in there. may be i am making some mistake
> in running the program or something like that!!! can anyone suggest
> any thing to solve the problem...thanking you all in advance.
>
>
>
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> Message: 3
> Date: Fri, 3 Jul 2009 20:12:37 +1000
> From: Itamar Kass <itamar.kass at gmail.com>
> Subject: Re: [gmx-users] waters in ion channels
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <c0962a4d0907030312x4b947700l66e349598d2009dd at mail.gmail.com>
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>
> Hi,
>
> I would say that those are water molecule which enter from the bulk
> water. This is normal and probably important for the physiological
> function of the system.
>
> Best,
> Itamar
>
> On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<samikbhat at yahoo.co.in
> > wrote:
> > hi i'm simulating a ion channel protein in DPPC membrane. i'm
> following
> > Justin's tutorial for that. and have completed upto the solvation
> step. but
> > right after solvation, i found some water molecules in the
> channel. now i
> > want to delete those molecules. in the tutorial it is advised tyo
> use the
> > keepbyz script to do that.. but after using that i didn't find
> any change
> > in the structure. watres are still present in there. may be i am
> making some
> > mistake in running the program or something like that!!! can
> anyone suggest
> > any thing to solve the problem...thanking you all in advance.
> >
> > ________________________________
> > Yahoo! recommends that you upgrade to the new and safer Internet
> Explorer 8.
> > _______________________________________________
> > 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
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 3 Jul 2009 12:19:48 +0200
> From: maria goranovic <mariagoranovic at gmail.com>
> Subject: [gmx-users] Re: how to center a MARTINI trajectory so that
> the lipid bilayer remains at the center of the box
> (XAvier Periole)
> To: gmx-users at gromacs.org
> Message-ID:
> <9024f1330907030319y77bc41e3wd3b4618959780b1b at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Well the bilayer drifts down in the z-direction, and eventually the
> leaflets
> almost separate, with each leaflet being on opposite ends of the box.
>
> if i try pbc nojump, the lipids drift far away from the box in the
> xy plane
>
> On Fri, Jul 3, 2009 at 12:00 PM, <gmx-users-request at gromacs.org>
> wrote:
>
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> >
> > Today's Topics:
> >
> > 1. Re: how to center a MARTINI trajectory so that the lipid
> > bilayer remains at the center of the box (XAvier Periole)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 3 Jul 2009 11:43:55 +0200
> > From: XAvier Periole <x.periole at rug.nl>
> > Subject: Re: [gmx-users] how to center a MARTINI trajectory so that
> > the lipid bilayer remains at the center of the box
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <EEA7DAA1-6584-4AF0-8321-3FEA30A413F4 at rug.nl>
> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> >
> >
> > What is the problem exactly? The two layers separate over the pbc?
> > did you try a -pbc nojump prior the centering?
> >
> > On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
> >
> > > Dear All,
> > >
> > > This has been discussed before for individual frames. But I am
> > > having a problem in trying to center a trajectory so that the
> > > bilayer remains at the center of the box. I have tried several
> > > combinations, but none of the them work. In each case, the
> centering
> > > and/or the fitting is done on the lipid bilayer itself.
> > >
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > center -boxcenter zero -pbc mol
> > >
> > > this one works for one particular .gro file, but not for the whole
> > > trajectory. I tried all of the following, but none of them work.
> > > What is the solution ?
> > >
> > >
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > center -boxcenter zero
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> pbc
> > > mol -boxcenter zero
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> pbc
> > > mol -center
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > pbc mol -fit trans
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > pbc mol -fit trans -center
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > pbc mol -fit trans -center -boxcenter zero
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> fit
> > > trans
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> fit
> > > progressive
> > >
> > > --
> > > Maria G.
> > > Technical University of Denmark
> > > Copenhagen
> > > _______________________________________________
> > > 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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> > > 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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> posting!
> >
> > End of gmx-users Digest, Vol 63, Issue 11
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> >
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
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> ------------------------------
>
> Message: 5
> Date: Fri, 3 Jul 2009 12:26:43 +0200
> From: XAvier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-users] Re: how to center a MARTINI trajectory so
> that the lipid bilayer remains at the center of the
> box (XAvier
> Periole)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1D610226-9AC2-419C-8233-633D4F1F1BEA at rug.nl>
> Content-Type: text/plain; charset="us-ascii"
>
>
> This sounds pretty bad! You have a drift of your all system
> apparently ...
> Did you not remove the COM of your system?
> For membranes it is often recommended to remove the water and the
> lipid bilayer separately. The might drift one from the other.
>
> On Jul 3, 2009, at 12:19 PM, maria goranovic wrote:
>
> > Well the bilayer drifts down in the z-direction, and eventually the
> > leaflets almost separate, with each leaflet being on opposite ends
> > of the box.
> >
> > if i try pbc nojump, the lipids drift far away from the box in the
> > xy plane
> >
> > On Fri, Jul 3, 2009 at 12:00 PM, <gmx-users-request at gromacs.org>
> > wrote:
> > Send gmx-users mailing list submissions to
> > gmx-users at gromacs.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gmx-users-request at gromacs.org
> >
> > You can reach the person managing the list at
> > gmx-users-owner at gromacs.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: how to center a MARTINI trajectory so that the lipid
> > bilayer remains at the center of the box (XAvier Periole)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 3 Jul 2009 11:43:55 +0200
> > From: XAvier Periole <x.periole at rug.nl>
> > Subject: Re: [gmx-users] how to center a MARTINI trajectory so that
> > the lipid bilayer remains at the center of the box
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <EEA7DAA1-6584-4AF0-8321-3FEA30A413F4 at rug.nl>
> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> >
> >
> > What is the problem exactly? The two layers separate over the pbc?
> > did you try a -pbc nojump prior the centering?
> >
> > On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
> >
> > > Dear All,
> > >
> > > This has been discussed before for individual frames. But I am
> > > having a problem in trying to center a trajectory so that the
> > > bilayer remains at the center of the box. I have tried several
> > > combinations, but none of the them work. In each case, the
> centering
> > > and/or the fitting is done on the lipid bilayer itself.
> > >
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > center -boxcenter zero -pbc mol
> > >
> > > this one works for one particular .gro file, but not for the whole
> > > trajectory. I tried all of the following, but none of them work.
> > > What is the solution ?
> > >
> > >
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > center -boxcenter zero
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> pbc
> > > mol -boxcenter zero
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> pbc
> > > mol -center
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > pbc mol -fit trans
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > pbc mol -fit trans -center
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > > pbc mol -fit trans -center -boxcenter zero
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> fit
> > > trans
> > > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> fit
> > > progressive
> > >
> > > --
> > > Maria G.
> > > Technical University of Denmark
> > > Copenhagen
> > > _______________________________________________
> > > 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
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > 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!
> >
> > End of gmx-users Digest, Vol 63, Issue 11
> > *****************************************
> >
> >
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> > _______________________________________________
> > 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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>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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