[gmx-users] different energies with different GROMACS versions
Dear all, I performed simple simulations of TIP4P-Ew water for 500 ps with three different GROMACS versions, namly 3.2.1, 3.3.1 and 4.0.2. There are 1000 molecules in the box and the temperature was 303 K at 1 bar. When I compare the total energies of the three equilibrated simulations I get: -38642.4 for GROMACS 4.0.2 -38638.2 for GROMACS 3.3.1 -38491.5 for GROMACS 3.2.1 So the 3.2.1 energies deviate by ca 150 kJ/mol from the other two. If I completly switsh off the coulomb interactions all energies are the same. Does anyone know a reason for that? I don't find anything about the 3.2.1 version at the web site. regards My top file and mdp files look like: [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name mass charge ptype c6 c12 ow15.99940 0.0 A 0.31643 0.68096 hw 1.00790 0.52422 A 0.0 0.0 vw 0.0-1.04844 A 0.0 0.0 [ nonbond_params ] ; ijfuncc6 c12 ow hw 10.00E+000.00E+00 ow vw 10.00E+000.00E+00 hw vw 10.00E+000.00E+00 [ moleculetype ] ; molname nrexcl SOL 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 ow1SOL ow10.0 15.99940 2 hw1SOL hw10.52422 1.00800 3 hw1SOL hw10.52422 1.00800 4 vw1SOL vw1 -1.04844 0.0 [ settles ] ; owfunct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; Dummy from funct ab 4 1 2 3 10.1066767208 0.1066767208 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [ system ] ; Name Converted from moscito [ molecules ] ; Compound#mols SOL 1000 and title = Yo cpp = /lib/cpp dt = 0.002 nsteps = 25 nstcomm = 1 nstxout = 0 nstvout = 0 nstxtcout = 100 nstlog = 1 nstenergy = 100 nstlist = 6 ns_type = grid coulombtype = pme fourierspacing = 0.12 pmeorder= 4 optimize_fft= yes ewald_rtol = 1.0e-5 DispCorr= EnerPres constraint_algorithm= lincs lincs_order = 4 lincs_iter = 3 lincs-warnangle = 30 rlist = 0.9 rvdw= 0.9 rcoulomb= 0.9 Tcoupl = nose-hoover tc-grps = sol ref_t = $T tau_t = 0.5 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 2.0 compressibility = 33.0e-6 ref_p = 1.0 gen_vel = no ;gen_temp= 303 ;gen_seed= 1993 ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein covalently bond to ligand
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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box
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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box
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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein covalently bond to ligand
Hi haziz...@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, hazizianhaziz...@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. ___ gmx-users mailing list gmx-us...@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-requ...@gromacs.org. 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 ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] waters in ion channels
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/___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] waters in ion channels
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 Bhattacharyasamikb...@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-us...@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)
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-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@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-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@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.peri...@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@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)
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-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@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-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@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.peri...@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@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] waters in ion channels
--- On Fri, 3/7/09, Itamar Kass itamar.k...@gmail.com wrote: From: Itamar Kass itamar.k...@gmail.com Subject: Re: [gmx-users] waters in ion channels To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 3 July, 2009, 3:42 PM 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 thank you a lot for the answar. one thing i would like to ask again that how can i be sure that those water molecules are not inside the hydrophobic core? and if they are not how deleting them could affect the system? thanks again Shamik On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharyasamikb...@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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)
://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 itamar.k...@gmail.com Subject: Re: [gmx-users] waters in ion channels To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: c0962a4d0907030312x4b947700l66e349598d200...@mail.gmail.com 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 Bhattacharyasamikb...@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 listgmx-users@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-requ...@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 mariagorano...@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@gromacs.org Message-ID: 9024f1330907030319y77bc41e3wd3b4618959780...@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-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@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-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@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.peri...@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@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@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
Re: [gmx-users] waters in ion channels
Hello, If you simply need to remove water molecules, you can simply use VMD, Pymol or whatever allows you to select and save atom coordinates in a format readable by gromacs. In VMD, I would do something like: set sel [atomselect top not (same resid as (water within 5 of resname DPPC)] or set sel [atomselect top not (water and same resid as (z20 and z80))] then animate write pdb myfile.pdb sel $sel That will select and save in a pdb file all but the water molecules too close to the lipids. Nicolas --- On Fri, 3/7/09, Itamar Kass itamar.k...@gmail.com wrote: From: Itamar Kass itamar.k...@gmail.com Subject: Re: [gmx-users] waters in ion channels To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, 3 July, 2009, 3:42 PM 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 thank you a lot for the answar. one thing i would like to ask again that how can i be sure that those water molecules are not inside the hydrophobic core? and if they are not how deleting them could affect the system? thanks again Shamik On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharyasamikb...@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44 ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: how to center a MARTINI trajectory so that thelipid bilayer remains at the center of the box (XAvier Periole)
Hello Xavier, and sorry to bump in. I am also having that same issue just as Maria described - could you please explain in a bit more details why does that happen? I mean, why does the membrane move along z-axis, and how to solve/avoid it? Thanks a lot, -Shay _ From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of XAvier Periole Sent: Friday, July 03, 2009 12:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: how to center a MARTINI trajectory so that thelipid bilayer remains at the center of the box (XAvier Periole) 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-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@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-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@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.peri...@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@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@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 listgmx-users@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
Re: [gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)
I remember having a similar issue a long time ago. If I remember correctly, the culprit was a bad parametrization of the Langevin piston. Maybe you should specified how the pressure is controlled, as well as how you managed the center of mass motions in you dynamics. Nicolas 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-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@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-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@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.peri...@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@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44 ___ gmx-users mailing listgmx-users@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
Re: [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)
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 itamar.k...@gmail.com Subject: Re: [gmx-users] waters in ion channels To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: c0962a4d0907030312x4b947700l66e349598d200...@mail.gmail.com 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 Bhattacharyasamikb...@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 listgmx-users@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-requ...@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 mariagorano...@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@gromacs.org Message-ID: 9024f1330907030319y77bc41e3wd3b4618959780...@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-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@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-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@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.peri...@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@gromacs.org Message-ID: eea7daa1-6584-4af0-8321-3fea30a41...@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
[gmx-users] long-bond warning during running
Dear all I am doing simulation of Dna-protein complex with using amber tools with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have made lot of changes in .pdb file after that pdb2gmx starts working but it give to many warnings. like- Warning: Long Bond (291-293 = 0.86645 nm) Warning: Long Bond (291-310 = 1.08462 nm) Warning: Long Bond (293-294 = 0.429679 nm) Warning: Long Bond (293-307 = 0.767604 nm) Warning: Long Bond (294-296 = 0.443442 nm) Warning: Long Bond (297-298 = 0.737835 nm) Warning: Long Bond (297-307 = 0.595315 nm) Warning: Long Bond (298-299 = 0.808366 nm) Warning: Long Bond (298-300 = 0.707622 nm) Warning: Long Bond (300-302 = 0.738664 nm) Warning: Long Bond (302-303 = 0.860242 nm) Warning: Long Bond (302-306 = 0.427252 nm) Warning: Long Bond (306-307 = 0.60875 nm) Warning: Long Bond (308-310 = 0.931786 nm) Warning: Long Bond (308-313 = 0.828688 nm) Warning: Long Bond (280-281 = 0.417096 nm) Warning: Long Bond (314-315 = 0.265962 nm) Warning: Long Bond (314-316 = 0.501846 nm) Warning: Long Bond (314-317 = 0.407156 nm) Warning: Long Bond (317-318 = 0.316267 nm) Warning: Long Bond (321-323 = 0.735348 nm) Warning: Long Bond (321-336 = 0.672012 nm) Warning: Long Bond (323-324 = 0.634508 nm) Warning: Long Bond (326-327 = 0.510123 nm) Warning: Long Bond (326-334 = 0.951643 nm) Warning: Long Bond (327-329 = 0.510298 nm) Warning: Long Bond (329-330 = 0.433539 nm) Warning: Long Bond (330-331 = 0.458922 nm) Warning: Long Bond (332-334 = 0.592297 nm) Warning: Long Bond (334-335 = 0.412661 nm) Warning: Long Bond (336-338 = 0.907703 nm) Warning: Long Bond (336-341 = 0.905717 nm) Warning: Long Bond (313-314 = 0.702567 nm) Warning: Long Bond (342-343 = 0.704904 nm) Warning: Long Bond (342-344 = 0.808923 nm) Warning: Long Bond (342-345 = 0.860233 nm) Warning: Long Bond (349-369 = 0.402523 nm) Warning: Long Bond (351-352 = 0.825131 nm) Warning: Long Bond (352-354 = 0.708667 nm) Warning: Long Bond (352-371 = 0.772094 nm) Warning: Long Bond (354-355 = 0.431195 nm) Warning: Long Bond (354-368 = 0.342288 nm) Warning: Long Bond (355-357 = 0.514821 nm) Warning: Long Bond (357-358 = 0.517131 nm) Warning: Long Bond (359-360 = 0.640538 nm) Warning: Long Bond (359-361 = 0.511957 nm) Warning: Long Bond (361-363 = 0.632475 nm) Warning: Long Bond (363-364 = 0.252832 nm) Warning: Long Bond (363-367 = 0.550244 nm) Warning: Long Bond (367-368 = 0.593196 nm) Warning: Long Bond (369-371 = 0.415453 nm) Warning: Long Bond (369-374 = 0.611634 nm) Warning: Long Bond (341-342 = 0.830307 nm) Warning: Long Bond (375-378 = 0.422488 nm) Warning: Long Bond (378-379 = 0.251446 nm) Warning: Short Bond (382-384 = 0.034 nm) Warning: Long Bond (382-397 = 0.360644 nm) Warning: Long Bond (384-385 = 0.448028 nm) Warning: Long Bond (385-387 = 0.854859 nm) Warning: Long Bond (385-399 = 0.898552 nm) Warning: Long Bond (387-388 = 0.341151 nm) Warning: Long Bond (387-395 = 0.64161 nm) Warning: Long Bond (388-390 = 0.583816 nm) Warning: Long Bond (390-391 = 0.460305 nm) Warning: Long Bond (391-393 = 0.596343 nm) Warning: Long Bond (393-395 = 0.510843 nm) Warning: Long Bond (395-396 = 0.378148 nm) Warning: Long Bond (397-399 = 0.922111 nm) Warning: Long Bond (397-402 = 0.596553 nm) Warning: Long Bond (374-375 = 0.40299 nm) Warning: Long Bond (403-404 = 0.637247 nm) Warning: Long Bond (404-407 = 0.318624 nm) Warning: Long Bond (407-409 = 0.379685 nm) Warning: Long Bond (407-426 = 0.543994 nm) Warning: Long Bond (409-410 = 0.500324 nm) Warning: Long Bond (410-428 = 0.609291 nm) Warning: Long Bond (412-425 = 0.788185 nm) Warning: Long Bond (413-415 = 0.791283 nm) Warning: Long Bond (415-416 = 0.708127 nm) Warning: Long Bond (416-417 = 0.255204 nm) Warning: Long Bond (416-425 = 0.715307 nm) Warning: Long Bond (417-418 = 0.618501 nm) Warning: Long Bond (417-421 = 0.670827 nm) Warning: Long Bond (421-422 = 0.950023 nm) Warning: Long Bond (422-424 = 0.717385 nm) Warning: Long Bond (424-425 = 1.08167 nm) Warning: Long Bond (426-428 = 0.511531 nm) Warning: Long Bond (426-431 = 1.08592 nm) Warning: Long Bond (432-433 = 0.912686 nm) Warning: Long Bond (432-435 = 0.519809 nm) Warning: Long Bond (435-436 = 0.450706 nm) Warning: Long Bond (436-439 = 0.325467 nm) Warning: Long Bond (439-441 = 0.719692 nm) Warning: Long Bond (439-456 = 0.856575 nm) Warning: Long Bond (441-442 = 0.700777 nm) Warning: Long Bond (442-444 = 0.617616 nm) Warning: Long Bond (442-458 = 0.526962 nm) Warning: Long Bond (444-445 = 0.608832 nm) Warning: Long Bond (444-454 = 0.466287 nm) Warning: Long Bond (447-449 = 0.719506 nm) Warning: Long Bond (449-453 = 0.400781 nm) Warning: Long Bond (454-455 = 0.781281 nm) Warning: Long Bond (456-458 = 0.43477 nm) Warning: Long Bond (456-461 = 0.854421 nm) Warning: Long Bond (431-432 = 1.14334 nm) Warning: Long Bond (462-463 = 0.675814 nm) Warning: Long Bond (462-464 = 0.429367 nm) Warning: Long Bond (462-465 = 0.92747 nm) Warning: Long Bond (465-466 = 0.61628 nm) Warning: Long Bond (466-469 = 0.813831 nm) Warning: Long Bond (469-471
[gmx-users] trouble with a triple bond
Dear all, I am experiencing some trouble with a small molecule containing a C-C triple bond, using a topology built by PRODRG beta. I intend to use ffG43a2, with a contraint on all bond lengths. Energy minization does not converge, as forces on the atoms involved in the bond seem to oscillate (not very high forces, though). Position restrained MD fails with LINCS errors, and unrestrained MD leads to a blow-up of the system. I guess the fault lies in the representation of the triple bond in the topology file, as a derivate of the molecule (with a single bond in the same place) works just fine. Excerpt from the itp building block provided by PRODRG beta. The triple bond is supposed to be between carbons 18 and 19: [ bonds ] ... 17 18 20.147 3422818.40.147 3422818.4 ; CAQ CAR18 19 20.122 2309822.80.122 2309822.8 ; CAR CAS20 19 20.147 3422818.40.147 3422818.4 ; CAT CAS ... [ angles ] ... 16 17 18 2109.5 520.0109.5 520.0 ; OAP CAQ CAR 17 18 19 2180.0 41840001.2180.0 41840001.2 ; CAQ CAR CAS 18 19 20 2180.0 41840001.2180.0 41840001.2 ; CAR CAS CAT 19 20 21 2109.5 520.0109.5 520.0 ; CAS CAT OAU ... There is no dihedral with 18 and 19 in the middle, but I assume that is correct as triple bonds are not supposed to be rotatable? What strikes me is the high force constant on the two 180 degree angles... may that be a source of error? Any help is appreciated! Maybe someone even has a working template of a correct triple bond topology at hand? Best regards and thank you for reading Alex PS: I also checked ffG43a2bon.itp, but I found nothing resembling a C-C triple bond... or maybe it's just the heat in my office. -- Alexander Bujotzek Zuse Institute Berlin Tel. : +49 30 84185-234 eMail: bujot...@zib.de ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box
Well .. I will rerun the simulations. setting this would do it, right: comm_grps = POPC Solvent where popc and solvent are the 2 groups ? -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] long-bond warning during running
nitu sharma wrote: Dear all You've broken something badly, like put the PDB information in columns of the wrong width. Mark I am doing simulation of Dna-protein complex with using amber tools with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have made lot of changes in .pdb file after that pdb2gmx starts working but it give to many warnings. like- Warning: Long Bond (291-293 = 0.86645 nm) Warning: Long Bond (291-310 = 1.08462 nm) Warning: Long Bond (293-294 = 0.429679 nm) Warning: Long Bond (293-307 = 0.767604 nm) Warning: Long Bond (294-296 = 0.443442 nm) Warning: Long Bond (297-298 = 0.737835 nm) Warning: Long Bond (297-307 = 0.595315 nm) Warning: Long Bond (298-299 = 0.808366 nm) Warning: Long Bond (298-300 = 0.707622 nm) Warning: Long Bond (300-302 = 0.738664 nm) Warning: Long Bond (302-303 = 0.860242 nm) Warning: Long Bond (302-306 = 0.427252 nm) Warning: Long Bond (306-307 = 0.60875 nm) Warning: Long Bond (308-310 = 0.931786 nm) Warning: Long Bond (308-313 = 0.828688 nm) Warning: Long Bond (280-281 = 0.417096 nm) Warning: Long Bond (314-315 = 0.265962 nm) Warning: Long Bond (314-316 = 0.501846 nm) Warning: Long Bond (314-317 = 0.407156 nm) Warning: Long Bond (317-318 = 0.316267 nm) Warning: Long Bond (321-323 = 0.735348 nm) Warning: Long Bond (321-336 = 0.672012 nm) Warning: Long Bond (323-324 = 0.634508 nm) Warning: Long Bond (326-327 = 0.510123 nm) Warning: Long Bond (326-334 = 0.951643 nm) Warning: Long Bond (327-329 = 0.510298 nm) Warning: Long Bond (329-330 = 0.433539 nm) Warning: Long Bond (330-331 = 0.458922 nm) Warning: Long Bond (332-334 = 0.592297 nm) Warning: Long Bond (334-335 = 0.412661 nm) Warning: Long Bond (336-338 = 0.907703 nm) Warning: Long Bond (336-341 = 0.905717 nm) Warning: Long Bond (313-314 = 0.702567 nm) Warning: Long Bond (342-343 = 0.704904 nm) Warning: Long Bond (342-344 = 0.808923 nm) Warning: Long Bond (342-345 = 0.860233 nm) Warning: Long Bond (349-369 = 0.402523 nm) Warning: Long Bond (351-352 = 0.825131 nm) Warning: Long Bond (352-354 = 0.708667 nm) Warning: Long Bond (352-371 = 0.772094 nm) Warning: Long Bond (354-355 = 0.431195 nm) Warning: Long Bond (354-368 = 0.342288 nm) Warning: Long Bond (355-357 = 0.514821 nm) Warning: Long Bond (357-358 = 0.517131 nm) Warning: Long Bond (359-360 = 0.640538 nm) Warning: Long Bond (359-361 = 0.511957 nm) Warning: Long Bond (361-363 = 0.632475 nm) Warning: Long Bond (363-364 = 0.252832 nm) Warning: Long Bond (363-367 = 0.550244 nm) Warning: Long Bond (367-368 = 0.593196 nm) Warning: Long Bond (369-371 = 0.415453 nm) Warning: Long Bond (369-374 = 0.611634 nm) Warning: Long Bond (341-342 = 0.830307 nm) Warning: Long Bond (375-378 = 0.422488 nm) Warning: Long Bond (378-379 = 0.251446 nm) Warning: Short Bond (382-384 = 0.034 nm) Warning: Long Bond (382-397 = 0.360644 nm) Warning: Long Bond (384-385 = 0.448028 nm) Warning: Long Bond (385-387 = 0.854859 nm) Warning: Long Bond (385-399 = 0.898552 nm) Warning: Long Bond (387-388 = 0.341151 nm) Warning: Long Bond (387-395 = 0.64161 nm) Warning: Long Bond (388-390 = 0.583816 nm) Warning: Long Bond (390-391 = 0.460305 nm) Warning: Long Bond (391-393 = 0.596343 nm) Warning: Long Bond (393-395 = 0.510843 nm) Warning: Long Bond (395-396 = 0.378148 nm) Warning: Long Bond (397-399 = 0.922111 nm) Warning: Long Bond (397-402 = 0.596553 nm) Warning: Long Bond (374-375 = 0.40299 nm) Warning: Long Bond (403-404 = 0.637247 nm) Warning: Long Bond (404-407 = 0.318624 nm) Warning: Long Bond (407-409 = 0.379685 nm) Warning: Long Bond (407-426 = 0.543994 nm) Warning: Long Bond (409-410 = 0.500324 nm) Warning: Long Bond (410-428 = 0.609291 nm) Warning: Long Bond (412-425 = 0.788185 nm) Warning: Long Bond (413-415 = 0.791283 nm) Warning: Long Bond (415-416 = 0.708127 nm) Warning: Long Bond (416-417 = 0.255204 nm) Warning: Long Bond (416-425 = 0.715307 nm) Warning: Long Bond (417-418 = 0.618501 nm) Warning: Long Bond (417-421 = 0.670827 nm) Warning: Long Bond (421-422 = 0.950023 nm) Warning: Long Bond (422-424 = 0.717385 nm) Warning: Long Bond (424-425 = 1.08167 nm) Warning: Long Bond (426-428 = 0.511531 nm) Warning: Long Bond (426-431 = 1.08592 nm) Warning: Long Bond (432-433 = 0.912686 nm) Warning: Long Bond (432-435 = 0.519809 nm) Warning: Long Bond (435-436 = 0.450706 nm) Warning: Long Bond (436-439 = 0.325467 nm) Warning: Long Bond (439-441 = 0.719692 nm) Warning: Long Bond (439-456 = 0.856575 nm) Warning: Long Bond (441-442 = 0.700777 nm) Warning: Long Bond (442-444 = 0.617616 nm) Warning: Long Bond (442-458 = 0.526962 nm) Warning: Long Bond (444-445 = 0.608832 nm) Warning: Long Bond (444-454 = 0.466287 nm) Warning: Long Bond (447-449 = 0.719506 nm) Warning: Long Bond (449-453 = 0.400781 nm) Warning: Long Bond (454-455 = 0.781281 nm) Warning: Long Bond (456-458 = 0.43477 nm) Warning: Long Bond (456-461 = 0.854421 nm) Warning: Long Bond (431-432 = 1.14334 nm) Warning: Long Bond (462-463 = 0.675814 nm) Warning: Long Bond (462-464 = 0.429367 nm) Warning: Long Bond (462-465 =
Re: [gmx-users] long-bond warning during running
nitu sharma wrote: Dear all I am doing simulation of Dna-protein complex with using amber tools with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have made lot of changes in .pdb file after that pdb2gmx starts working but it give to many warnings. like- Please consult the wiki: http://oldwiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms -Justin Warning: Long Bond (291-293 = 0.86645 nm) Warning: Long Bond (291-310 = 1.08462 nm) Warning: Long Bond (293-294 = 0.429679 nm) Warning: Long Bond (293-307 = 0.767604 nm) Warning: Long Bond (294-296 = 0.443442 nm) Warning: Long Bond (297-298 = 0.737835 nm) Warning: Long Bond (297-307 = 0.595315 nm) Warning: Long Bond (298-299 = 0.808366 nm) Warning: Long Bond (298-300 = 0.707622 nm) Warning: Long Bond (300-302 = 0.738664 nm) Warning: Long Bond (302-303 = 0.860242 nm) Warning: Long Bond (302-306 = 0.427252 nm) Warning: Long Bond (306-307 = 0.60875 nm) Warning: Long Bond (308-310 = 0.931786 nm) Warning: Long Bond (308-313 = 0.828688 nm) Warning: Long Bond (280-281 = 0.417096 nm) Warning: Long Bond (314-315 = 0.265962 nm) Warning: Long Bond (314-316 = 0.501846 nm) Warning: Long Bond (314-317 = 0.407156 nm) Warning: Long Bond (317-318 = 0.316267 nm) Warning: Long Bond (321-323 = 0.735348 nm) Warning: Long Bond (321-336 = 0.672012 nm) Warning: Long Bond (323-324 = 0.634508 nm) Warning: Long Bond (326-327 = 0.510123 nm) Warning: Long Bond (326-334 = 0.951643 nm) Warning: Long Bond (327-329 = 0.510298 nm) Warning: Long Bond (329-330 = 0.433539 nm) Warning: Long Bond (330-331 = 0.458922 nm) Warning: Long Bond (332-334 = 0.592297 nm) Warning: Long Bond (334-335 = 0.412661 nm) Warning: Long Bond (336-338 = 0.907703 nm) Warning: Long Bond (336-341 = 0.905717 nm) Warning: Long Bond (313-314 = 0.702567 nm) Warning: Long Bond (342-343 = 0.704904 nm) Warning: Long Bond (342-344 = 0.808923 nm) Warning: Long Bond (342-345 = 0.860233 nm) Warning: Long Bond (349-369 = 0.402523 nm) Warning: Long Bond (351-352 = 0.825131 nm) Warning: Long Bond (352-354 = 0.708667 nm) Warning: Long Bond (352-371 = 0.772094 nm) Warning: Long Bond (354-355 = 0.431195 nm) Warning: Long Bond (354-368 = 0.342288 nm) Warning: Long Bond (355-357 = 0.514821 nm) Warning: Long Bond (357-358 = 0.517131 nm) Warning: Long Bond (359-360 = 0.640538 nm) Warning: Long Bond (359-361 = 0.511957 nm) Warning: Long Bond (361-363 = 0.632475 nm) Warning: Long Bond (363-364 = 0.252832 nm) Warning: Long Bond (363-367 = 0.550244 nm) Warning: Long Bond (367-368 = 0.593196 nm) Warning: Long Bond (369-371 = 0.415453 nm) Warning: Long Bond (369-374 = 0.611634 nm) Warning: Long Bond (341-342 = 0.830307 nm) Warning: Long Bond (375-378 = 0.422488 nm) Warning: Long Bond (378-379 = 0.251446 nm) Warning: Short Bond (382-384 = 0.034 nm) Warning: Long Bond (382-397 = 0.360644 nm) Warning: Long Bond (384-385 = 0.448028 nm) Warning: Long Bond (385-387 = 0.854859 nm) Warning: Long Bond (385-399 = 0.898552 nm) Warning: Long Bond (387-388 = 0.341151 nm) Warning: Long Bond (387-395 = 0.64161 nm) Warning: Long Bond (388-390 = 0.583816 nm) Warning: Long Bond (390-391 = 0.460305 nm) Warning: Long Bond (391-393 = 0.596343 nm) Warning: Long Bond (393-395 = 0.510843 nm) Warning: Long Bond (395-396 = 0.378148 nm) Warning: Long Bond (397-399 = 0.922111 nm) Warning: Long Bond (397-402 = 0.596553 nm) Warning: Long Bond (374-375 = 0.40299 nm) Warning: Long Bond (403-404 = 0.637247 nm) Warning: Long Bond (404-407 = 0.318624 nm) Warning: Long Bond (407-409 = 0.379685 nm) Warning: Long Bond (407-426 = 0.543994 nm) Warning: Long Bond (409-410 = 0.500324 nm) Warning: Long Bond (410-428 = 0.609291 nm) Warning: Long Bond (412-425 = 0.788185 nm) Warning: Long Bond (413-415 = 0.791283 nm) Warning: Long Bond (415-416 = 0.708127 nm) Warning: Long Bond (416-417 = 0.255204 nm) Warning: Long Bond (416-425 = 0.715307 nm) Warning: Long Bond (417-418 = 0.618501 nm) Warning: Long Bond (417-421 = 0.670827 nm) Warning: Long Bond (421-422 = 0.950023 nm) Warning: Long Bond (422-424 = 0.717385 nm) Warning: Long Bond (424-425 = 1.08167 nm) Warning: Long Bond (426-428 = 0.511531 nm) Warning: Long Bond (426-431 = 1.08592 nm) Warning: Long Bond (432-433 = 0.912686 nm) Warning: Long Bond (432-435 = 0.519809 nm) Warning: Long Bond (435-436 = 0.450706 nm) Warning: Long Bond (436-439 = 0.325467 nm) Warning: Long Bond (439-441 = 0.719692 nm) Warning: Long Bond (439-456 = 0.856575 nm) Warning: Long Bond (441-442 = 0.700777 nm) Warning: Long Bond (442-444 = 0.617616 nm) Warning: Long Bond (442-458 = 0.526962 nm) Warning: Long Bond (444-445 = 0.608832 nm) Warning: Long Bond (444-454 = 0.466287 nm) Warning: Long Bond (447-449 = 0.719506 nm) Warning: Long Bond (449-453 = 0.400781 nm) Warning: Long Bond (454-455 = 0.781281 nm) Warning: Long Bond (456-458 = 0.43477 nm) Warning: Long Bond (456-461 = 0.854421 nm) Warning: Long Bond (431-432 = 1.14334 nm) Warning: Long Bond (462-463 = 0.675814 nm) Warning: Long Bond (462-464 = 0.429367 nm) Warning:
RE: [gmx-users] waters in ion channels
You may not want to delete those molecules. It will be interesting to see, whether they stay or leave throughout the MD simulation after some time. My experience with the Sybyl software was that after some energy minimization (thus removing large forces that could have repelled the waters out the channel) the water molecules leave the pore and return to the bulk of the solvent. Then it is a real physical effect, if not an artifact of the applied force-field or simulation conditions. Nonetheless, I would wait with deleteing these water molecules and see what happens after, e.g. 200-300 ps. Best regards Peter Nagy Dept. medicnal and Biological Chemistry The Univ. Toledo, Toledo, OH, USA From: gmx-users-boun...@gromacs.org on behalf of Samik Bhattacharya Sent: Fri 7/3/2009 6:08 AM To: Gromacs Subject: [gmx-users] waters in ion channels 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 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/ . ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trouble with a triple bond
Maybe this previous post will be of some use: http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html -Justin Alexander Bujotzek wrote: Dear all, I am experiencing some trouble with a small molecule containing a C-C triple bond, using a topology built by PRODRG beta. I intend to use ffG43a2, with a contraint on all bond lengths. Energy minization does not converge, as forces on the atoms involved in the bond seem to oscillate (not very high forces, though). Position restrained MD fails with LINCS errors, and unrestrained MD leads to a blow-up of the system. I guess the fault lies in the representation of the triple bond in the topology file, as a derivate of the molecule (with a single bond in the same place) works just fine. Excerpt from the itp building block provided by PRODRG beta. The triple bond is supposed to be between carbons 18 and 19: [ bonds ] ... 17 18 20.147 3422818.40.147 3422818.4 ; CAQ CAR18 19 20.122 2309822.80.122 2309822.8 ; CAR CAS20 19 20.147 3422818.40.147 3422818.4 ; CAT CAS ... [ angles ] ... 16 17 18 2109.5 520.0109.5 520.0 ; OAP CAQ CAR 17 18 19 2180.0 41840001.2180.0 41840001.2 ; CAQ CAR CAS 18 19 20 2180.0 41840001.2180.0 41840001.2 ; CAR CAS CAT 19 20 21 2109.5 520.0109.5 520.0 ; CAS CAT OAU ... There is no dihedral with 18 and 19 in the middle, but I assume that is correct as triple bonds are not supposed to be rotatable? What strikes me is the high force constant on the two 180 degree angles... may that be a source of error? Any help is appreciated! Maybe someone even has a working template of a correct triple bond topology at hand? Best regards and thank you for reading Alex PS: I also checked ffG43a2bon.itp, but I found nothing resembling a C-C triple bond... or maybe it's just the heat in my office. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box
I would first check that the COM motion ... before reruning! You might endup with the same problem if this is not the issue! On Jul 3, 2009, at 3:26 PM, maria goranovic wrote: Well .. I will rerun the simulations. setting this would do it, right: comm_grps = POPC Solvent where popc and solvent are the 2 groups ? -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with user-defined potentials
Hello, I'm getting problems to simulate amorphous silica with potentials I made myself : table_Si_Si.xvg, table_Si_O.xvg, table_O_O.xvg and table.xvg (which should not be used as all the possible non-bonded interactions are given in the three previous tables). The generation of the topology file with grompp works well but when I'm try to simulate my system (mdrun), Im getting a segmentation fault. Am I missing something in the topology file or grompp.mdp file ? I just want to have the non-bonded interactions defined in my tables to be applied. My topology and input file are hereafter. I can give you my tables.xvg but they are too big to be posted on the forum. Thanks a lot My topology file TOPOL.TOP is the following : [ defaults ] 2 1 0 [ atomtypes ] ; name mass charge ptype c6c12 O 15.99940 -0.955209 A 1.0 1.0 0.; Si 28.08550 1.910418 A 1.0 1.0 0.; [ nonbond_params ] O O 2 1 1 1 O Si 2 1 1 1 Si Si 2 1 1 1 [ moleculetype ] O 0 [ atoms ] 1 O 1 OO 1 -0.955209 15.99940 [ moleculetype ] Si 0; [ atoms ] 1 Si 1 Si Si 21.910418 28.08550 [ system ] Silica [ molecules ] O384 Si 192 and my mdrun input file GROMPP.MDP is : title = 576-atoms a-SiO2 model 01 cpp = cpp define = integrator = md dt = 0.001 nsteps = 25000 ; Coulomb type coulombtype = User vdwtype = User rvdw= 1.0 rlist = 1.0 rcoulomb= 1.0 fourierspacing = 0.1 ewald_rtol = 1e-5 energygrps = Si O energygrp_table = Si Si Si O O O ; Temperature Coupling tcoupl = nose-hoover tc_grps = System tau_t = 0.02 ref_t = 7000 gen_vel = yes gen_temp= 7000 gen_seed= -1 ; Simulated Annealing ; annealing = single ; annealing_npoints = 3 ; annealing_time = 0 56 150 ; annealing_temp = 5000 5000 300 ; Output parameters nstxout = 100 nstxtcout = 1000 -- --- David Waroquiers, Phd Student European Theoretical Spectroscopy Facility (ETSF) Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain (UCL) --- Address : Bâtiment Boltzmann Place Croix du Sud, 1 1348 Louvain-la-Neuve, Belgique --- E-mail : david.waroqui...@uclouvain.be Tel : + 32 (0)10 / 47 28 38 Fax : + 32 (0)10 / 47 34 52 --- ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fast energy parameter
Hi guys, i'm working on binding energy of two proteins. I will try to use thermidynamic integration, but i'm afraid that this will take long time of computing, and I just reading and learning about TI or other methods for free energy calculation, so this will be a long time project However, while I try to put the MD to work for this methods, i need to know if there is another, maybe not very accurated, energy parameter, derived from GROMACS MD to take into account before the TI attemp. I'll wait for your suggestions Thanks Felipe Villanelo Lizana Laboratorio de Biología Estructural y Molecular (BEM) Universidad de Chile ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fast energy parameter
Felipe Villanelo wrote: Hi guys, i'm working on binding energy of two proteins. I will try to use thermidynamic integration, but i'm afraid that this will take long time of computing, and I just reading and learning about TI or other methods for free energy calculation, so this will be a long time project However, while I try to put the MD to work for this methods, i need to know if there is another, maybe not very accurated, energy parameter, derived from GROMACS MD to take into account before the TI attemp. Free energy of binding of two proteins in explicit solvent will indeed be an expensive computation. The obvious cheap alternative is the free energy of binding in implicit solvent, which will be orders of magnitude cheaper. You can't use GROMACS though... try APBS. Mark ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with user-defined potentials
David Waroquiers wrote: Hello, I'm getting problems to simulate amorphous silica with potentials I made myself : table_Si_Si.xvg, table_Si_O.xvg, table_O_O.xvg and table.xvg (which should not be used as all the possible non-bonded interactions are given in the three previous tables). The generation of the topology file with grompp works well but when I'm try to simulate my system (mdrun), Im getting a segmentation fault. It's vanishingly rare for GROMACS to segfault without an error message. Consult all of stdout, stderr and your .log file for messages. Probably, your combination of starting configuration and model physics are broken. If you're confident your starting configuration is good (e.g. you know it works with some other Si-O force field) then you'll have to go over your table files, I suppose. Mark Am I missing something in the topology file or grompp.mdp file ? I just want to have the non-bonded interactions defined in my tables to be applied. My topology and input file are hereafter. I can give you my tables.xvg but they are too big to be posted on the forum. Thanks a lot My topology file TOPOL.TOP is the following : [ defaults ] 2 1 0 [ atomtypes ] ; name mass charge ptype c6c12 O 15.99940 -0.955209 A 1.0 1.0 0.; Si 28.08550 1.910418 A 1.0 1.0 0.; [ nonbond_params ] O O 2 1 1 1 O Si 2 1 1 1 Si Si 2 1 1 1 [ moleculetype ] O 0 [ atoms ] 1 O 1 OO 1 -0.955209 15.99940 [ moleculetype ] Si 0; [ atoms ] 1 Si 1 Si Si 21.910418 28.08550 [ system ] Silica [ molecules ] O384 Si 192 and my mdrun input file GROMPP.MDP is : title = 576-atoms a-SiO2 model 01 cpp = cpp define = integrator = md dt = 0.001 nsteps = 25000 ; Coulomb type coulombtype = User vdwtype = User rvdw= 1.0 rlist = 1.0 rcoulomb= 1.0 fourierspacing = 0.1 ewald_rtol = 1e-5 energygrps = Si O energygrp_table = Si Si Si O O O ; Temperature Coupling tcoupl = nose-hoover tc_grps = System tau_t = 0.02 ref_t = 7000 gen_vel = yes gen_temp= 7000 gen_seed= -1 ; Simulated Annealing ; annealing = single ; annealing_npoints = 3 ; annealing_time = 0 56 150 ; annealing_temp = 5000 5000 300 ; Output parameters nstxout = 100 nstxtcout = 1000 ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] puzzling about adding H atoms
Dear gmx users, Through the manual, I learn of that both pdb2gmx and protonate can add H atoms according to the hdb files. About it, I have some puzzles as follows: Are the two programs equivalent in adding H atoms? If it is yes, why bother to develop another program? It seems that protonate program can not generate partial atom charges, so after protonation, it still needs to do so. Thanks a lot ahead for any reply. Best regards Chaofu Wu _ Messenger10年嘉年华，礼品大奖等你拿！ http://10.msn.com.cn___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] puzzling about adding H atoms
wuxiao wrote: Dear gmx users, Through the manual, I learn of that both pdb2gmx and protonate can add H atoms according to the hdb files. About it, I have some puzzles as follows: Are the two programs equivalent in adding H atoms? If it is yes, why bother to develop another program? It seems that protonate program can not generate partial atom charges, so after protonation, it still needs to do so. Using pdb2gmx will add only the H atoms specified by the force field - for UA force fields this is polar H atoms only. Using protonate will add all H atoms according to valence requirements of all atoms (i.e., a CH2 group would get 2 H atoms, while in a UA force field, no H atoms would be present). -Justin Thanks a lot ahead for any reply. Best regards Chaofu Wu 立刻下载 MSN 保护盾，保障Messenger 安全稳定！ 现在就下载！ http://im.live.cn/safe/ ___ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
