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 ?
Is this just a problem which can be corrected after the simulation, or are the simulations now completely useless ? -MAria On Fri, Jul 3, 2009 at 12:27 PM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > 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 > [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: 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 <[email protected]> > Subject: Re: [gmx-users] protein covalently bond to ligand > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi [email protected], > > 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<[email protected]> 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. > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > 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 <[email protected]> > Subject: [gmx-users] waters in ion channels > To: Gromacs <[email protected]> > Message-ID: <[email protected]> > 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. > > > > Looking for local information? Find it on Yahoo! Local > http://in.local.yahoo.com/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/266f5139/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Fri, 3 Jul 2009 20:12:37 +1000 > From: Itamar Kass <[email protected]> > Subject: Re: [gmx-users] waters in ion channels > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > 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<[email protected]> > 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 [email protected] > > 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 [email protected]. > > 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 <[email protected]> > 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: [email protected] > Message-ID: > <[email protected]> > 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, <[email protected]> wrote: > > > Send gmx-users mailing list submissions to > > [email protected] > > > > 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 > > [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: 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 <[email protected]> > > 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 <[email protected]> > > Message-ID: <[email protected]> > > 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 [email protected] > > > 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 [email protected]. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------ > > > > _______________________________________________ > > gmx-users mailing list > > [email protected] > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/e16931da/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Fri, 3 Jul 2009 12:26:43 +0200 > From: XAvier Periole <[email protected]> > 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 <[email protected]> > Message-ID: <[email protected]> > 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, <[email protected]> > > wrote: > > Send gmx-users mailing list submissions to > > [email protected] > > > > 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 > > [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: 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 <[email protected]> > > 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 <[email protected]> > > Message-ID: <[email protected]> > > 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 [email protected] > > > 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 [email protected]. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------ > > > > _______________________________________________ > > gmx-users mailing list > > [email protected] > > 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 [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/1aec8a26/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > 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 12 > ***************************************** > -- Maria G. Technical University of Denmark Copenhagen
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