Re: [gmx-users] grommp warning
Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am using option com Is it right As per your answer in these archieve... http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html Under NPT the box size changes each step. You are using position restraints to a pre-defined set of reference coordinates. This option allows you to choose how those *reference coordinates* should change when the box size changes (respectively do not scale them at all, scale them all, or scale their COM but leave their internal geometry fixed). Position restraints are then applied using the updated reference coordinates. In some archives I found if any one used freeze group suggested to use refcoord_scaling = no When we applied position restrain, the position of backbone atom is restrained.. I make my assumption as like follow.. No = no scalling in position of atoms.(system maintain rigidity). all = the system bcome flexible com= ? ( scalling com means changing com co-ordinates or something else) I get confused Please accept my apology for stupid question Please help to come out through the confusion. With best wishes and regards Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] grommp warning
On 15/08/2012 4:52 PM, rama david wrote: Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am using option com Is it right Probably. That's up to you. Only you know your overall objective about why you want to use PR and NPT. As per your answer in these archieve... http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html Under NPT the box size changes each step. You are using position restraints to a pre-defined set of reference coordinates. This option allows you to choose how those *reference coordinates* should change when the box size changes (respectively do not scale them at all, scale them all, or scale their COM but leave their internal geometry fixed). Position restraints are then applied using the updated reference coordinates. In some archives I found if any one used freeze group suggested to use refcoord_scaling = no When we applied position restrain, the position of backbone atom is restrained.. I make my assumption as like follow.. No = no scalling in position of atoms.(system maintain rigidity). all = the system bcome flexible com= ? ( scalling com means changing com co-ordinates or something else) There's a definition in manual 7.3... what else are you asking for? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] my VMD
Dear All, I just installed a VMD. And then I load a gro file and a xtc file from a simulation. The bar in the VMD Main window continuously moves, however the protein molecule in the OpenGL Display window does not move. Will you please tell me what is the problem, or how can see the whole simulation? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] box of simulation
Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8 3- grompp -f em.mdp -c solute1501.gro -p topol.top -o em1.tpr 4- mdrun -v -deffnm em1 5- genbox -cp em1.gro -cs cyclohexane.gro -o solutecyc.gro -maxsol 8870 6- grompp -f em.mdp -c solutecyc.gro -p topol.top -o em2.tpr 7- mdrun -v -deffnm em2 8- genion -s em2.tpr -o solutecycion.gro -p topol.top -nname BR- -nn 150 9- grompp -f em.mdp -c solutecycion.gro -p topol.top -o em3.tpr 10- mdrun -v -deffnm em3 11- grompp -f pr.mdp -c em3.gro -p topol.top -o pr.tpr 12- mdrun -v -deffnm pr And topology file has been justified with correct numbers for component. After equilibrium (NPT ensemble), size of box change to 12.45*12.45*12.45, but before equilibrium at step 6 had an error, if I had defined size smaller than 13.6*13.6*13.6 and it couldn't place 8870 cyclohexane into the box!!! May I ask you to say me where is my problem, Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Parameters for bonded interactions
Thanks a lot Mark! Date: Wed, 15 Aug 2012 11:48:00 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Parameters for bonded interactions On 15/08/2012 9:46 AM, Sebastien Cote wrote: Dear Gromacs users, In the topology file of the protein, we see every two atoms that share a bond, three atoms that share a bond angle, and four atoms that share a torsion angle. However, the parameters (equilibrium value, energy constant, phase) are not explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is there a simple way to see (without having to look at the code) which parameters are associated to which bond length, bond angle and torsion angle? More specifically, I would like to know which torsion angle parameters is specifically associated to each torsion angle. In the ffbonded table, there is sometimes different groups of four atoms that can be associated to the same torsion angle as there is the 'X' atom which can be any atom. grompp -pp writes out a post-processed topology, which may be what you need. Otherwise you can inspect the contents of the .tpr file to see which interaction gets which parameters. That is not easy for a large system, but is definitive. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Parameters for bonded interactions
After checking the post-processed topology, it does not contain the information that I need. I would like to know the torsion angle parameters of each torsion angle, and then compare with the ffbonded file to see the corresponding four-atom groups ' X X X X '. Is there a way to convert the .tpr file to 'human readable'? Thanks again, Sebastien Date: Wed, 15 Aug 2012 11:48:00 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Parameters for bonded interactions On 15/08/2012 9:46 AM, Sebastien Cote wrote: Dear Gromacs users, In the topology file of the protein, we see every two atoms that share a bond, three atoms that share a bond angle, and four atoms that share a torsion angle. However, the parameters (equilibrium value, energy constant, phase) are not explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is there a simple way to see (without having to look at the code) which parameters are associated to which bond length, bond angle and torsion angle? More specifically, I would like to know which torsion angle parameters is specifically associated to each torsion angle. In the ffbonded table, there is sometimes different groups of four atoms that can be associated to the same torsion angle as there is the 'X' atom which can be any atom. grompp -pp writes out a post-processed topology, which may be what you need. Otherwise you can inspect the contents of the .tpr file to see which interaction gets which parameters. That is not easy for a large system, but is definitive. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Parameters for bonded interactions
On 15/08/2012 8:44 PM, Sebastien Cote wrote: After checking the post-processed topology, it does not contain the information that I need. I would like to know the torsion angle parameters of each torsion angle, and then compare with the ffbonded file to see the corresponding four-atom groups ' X X X X '. Is there a way to convert the .tpr file to 'human readable'? Sorry, meant to say that last email. gmxdump is all that is available. You'll have to work backwards from the atom numbers (starting counting from zero!) to get the interaction number to look up the interaction parameters from their list. Mark Thanks again, Sebastien Date: Wed, 15 Aug 2012 11:48:00 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Parameters for bonded interactions On 15/08/2012 9:46 AM, Sebastien Cote wrote: Dear Gromacs users, In the topology file of the protein, we see every two atoms that share a bond, three atoms that share a bond angle, and four atoms that share a torsion angle. However, the parameters (equilibrium value, energy constant, phase) are not explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is there a simple way to see (without having to look at the code) which parameters are associated to which bond length, bond angle and torsion angle? More specifically, I would like to know which torsion angle parameters is specifically associated to each torsion angle. In the ffbonded table, there is sometimes different groups of four atoms that can be associated to the same torsion angle as there is the 'X' atom which can be any atom. grompp -pp writes out a post-processed topology, which may be what you need. Otherwise you can inspect the contents of the .tpr file to see which interaction gets which parameters. That is not easy for a large system, but is definitive. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] box of simulation
Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8 3- grompp -f em.mdp -c solute1501.gro -p topol.top -o em1.tpr 4- mdrun -v -deffnm em1 5- genbox -cp em1.gro -cs cyclohexane.gro -o solutecyc.gro -maxsol 8870 6- grompp -f em.mdp -c solutecyc.gro -p topol.top -o em2.tpr 7- mdrun -v -deffnm em2 8- genion -s em2.tpr -o solutecycion.gro -p topol.top -nname BR- -nn 150 9- grompp -f em.mdp -c solutecycion.gro -p topol.top -o em3.tpr 10- mdrun -v -deffnm em3 11- grompp -f pr.mdp -c em3.gro -p topol.top -o pr.tpr 12- mdrun -v -deffnm pr And topology file has been justified with correct numbers for component. After equilibrium (NPT ensemble), size of box change to 12.45*12.45*12.45, but before equilibrium at step 6 had an error, if I had defined size smaller than 13.6*13.6*13.6 and it couldn't place 8870 cyclohexane into the box!!! May I ask you to say me where is my problem, Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Parameters for bonded interactions
Thanks Mark! This is exactly what I need. Date: Wed, 15 Aug 2012 22:18:10 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Parameters for bonded interactions On 15/08/2012 8:44 PM, Sebastien Cote wrote: After checking the post-processed topology, it does not contain the information that I need. I would like to know the torsion angle parameters of each torsion angle, and then compare with the ffbonded file to see the corresponding four-atom groups ' X X X X '. Is there a way to convert the .tpr file to 'human readable'? Sorry, meant to say that last email. gmxdump is all that is available. You'll have to work backwards from the atom numbers (starting counting from zero!) to get the interaction number to look up the interaction parameters from their list. Mark Thanks again, Sebastien Date: Wed, 15 Aug 2012 11:48:00 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Parameters for bonded interactions On 15/08/2012 9:46 AM, Sebastien Cote wrote: Dear Gromacs users, In the topology file of the protein, we see every two atoms that share a bond, three atoms that share a bond angle, and four atoms that share a torsion angle. However, the parameters (equilibrium value, energy constant, phase) are not explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is there a simple way to see (without having to look at the code) which parameters are associated to which bond length, bond angle and torsion angle? More specifically, I would like to know which torsion angle parameters is specifically associated to each torsion angle. In the ffbonded table, there is sometimes different groups of four atoms that can be associated to the same torsion angle as there is the 'X' atom which can be any atom. grompp -pp writes out a post-processed topology, which may be what you need. Otherwise you can inspect the contents of the .tpr file to see which interaction gets which parameters. That is not easy for a large system, but is definitive. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] box of simulation
On 15/08/2012 10:27 PM, mohammad agha wrote: Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8 3- grompp -f em.mdp -c solute1501.gro -p topol.top -o em1.tpr 4- mdrun -v -deffnm em1 5- genbox -cp em1.gro -cs cyclohexane.gro -o solutecyc.gro -maxsol 8870 6- grompp -f em.mdp -c solutecyc.gro -p topol.top -o em2.tpr 7- mdrun -v -deffnm em2 8- genion -s em2.tpr -o solutecycion.gro -p topol.top -nname BR- -nn 150 9- grompp -f em.mdp -c solutecycion.gro -p topol.top -o em3.tpr 10- mdrun -v -deffnm em3 11- grompp -f pr.mdp -c em3.gro -p topol.top -o pr.tpr 12- mdrun -v -deffnm pr And topology file has been justified with correct numbers for component. After equilibrium (NPT ensemble), size of box change to 12.45*12.45*12.45, but before equilibrium at step 6 had an error, if I had defined size smaller than 13.6*13.6*13.6 and it couldn't place 8870 cyclohexane into the box!!! May I ask you to say me where is my problem, Please? You're solvating 150 randomly placed molecules with cyclohexane using genbox. genbox just overlays the coordinates in the two boxes, and removes the overlapping solvent molecules. You have so much surface area of solute and such a large solvent that you're certain to have lots of voids in your solvated system where genbox was unable to fit them around each other. Hence the density will be wrong. So you need a more cunning approach. g_membed is intended for solvating a protein with a membrane, which has the same kind of issues you are seeing, so you may be able to adapt that for your needs. There are other methods out there, I believe. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Topology file
Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_D.itp #include topol_Protein_chain_E.itp #include topol_Protein_chain_F.itp #include topol_Protein_chain_G.itp ;Include ligand topology #include FDP_Dp.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Topology file
Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_D.itp #include topol_Protein_chain_E.itp #include topol_Protein_chain_F.itp #include topol_Protein_chain_G.itp ;Include ligand topology #include FDP_Dp.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] box of simulation
Dear Mark, Thank you very much from your help. Best Regards Sara - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, August 15, 2012 5:23 PM Subject: Re: [gmx-users] box of simulation On 15/08/2012 10:27 PM, mohammad agha wrote: Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8 3- grompp -f em.mdp -c solute1501.gro -p topol.top -o em1.tpr 4- mdrun -v -deffnm em1 5- genbox -cp em1.gro -cs cyclohexane.gro -o solutecyc.gro -maxsol 8870 6- grompp -f em.mdp -c solutecyc.gro -p topol.top -o em2.tpr 7- mdrun -v -deffnm em2 8- genion -s em2.tpr -o solutecycion.gro -p topol.top -nname BR- -nn 150 9- grompp -f em.mdp -c solutecycion.gro -p topol.top -o em3.tpr 10- mdrun -v -deffnm em3 11- grompp -f pr.mdp -c em3.gro -p topol.top -o pr.tpr 12- mdrun -v -deffnm pr And topology file has been justified with correct numbers for component. After equilibrium (NPT ensemble), size of box change to 12.45*12.45*12.45, but before equilibrium at step 6 had an error, if I had defined size smaller than 13.6*13.6*13.6 and it couldn't place 8870 cyclohexane into the box!!! May I ask you to say me where is my problem, Please? You're solvating 150 randomly placed molecules with cyclohexane using genbox. genbox just overlays the coordinates in the two boxes, and removes the overlapping solvent molecules. You have so much surface area of solute and such a large solvent that you're certain to have lots of voids in your solvated system where genbox was unable to fit them around each other. Hence the density will be wrong. So you need a more cunning approach. g_membed is intended for solvating a protein with a membrane, which has the same kind of issues you are seeing, so you may be able to adapt that for your needs. There are other methods out there, I believe. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Topology file
On 8/15/12 9:12 AM, Ankita naithani wrote: Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? Yes, #include statements for position restraint files are contained in each chain topology. -Justin On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_D.itp #include topol_Protein_chain_E.itp #include topol_Protein_chain_F.itp #include topol_Protein_chain_G.itp ;Include ligand topology #include FDP_Dp.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Cross-correlation maps
Dear Gromacs users! I want to obtain Cross-correlation maps ( for indication of the cross-correlated fluctuations of the residues). The example of such maps can be found here http://pubs.acs.org/doi/abs/10.1021/ja076046a I found that modificied version of the G_covar from users contributions can do such things. But because of the older version of that program (3.3.3) I've obtained the below error using it with 4.5.5 gromacs Reading file md_GO.tpr, VERSION 4.5.5 (single precision) --- Program g_covar_mod, VERSION 3.3.3 Source code file: tpxio.c, line: 1192 Fatal error: reading tpx file (md_GO.tpr) version 73 with version 40 program --- Is there newest versions of the G_covar for such things or alternativelly any others ways to calculate such correlations maps ? Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] when?
hello: Does anybody have any idea for the new version? when would it be reachable? and what's new? thx Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] when?
On Wed, Aug 15, 2012 at 4:31 PM, Albert mailmd2...@gmail.com wrote: hello: Does anybody have any idea for the new version? when would it be reachable? and what's new? You can always try the current version of any of the branches using Git: http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage There you can access the latest versions of the 4.5, 4.6 and master branches. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] when?
hello: that's for kind reply. The unreleased version probably is not stable enough. I am asking for the official released version. As we can see the 4.5.5 is the one which was released almost one year ago. Do you have any idea when the next version would be officially released? And what's new comparing with current 4.5.5? thx best A. On 08/15/2012 04:39 PM, Elton Carvalho wrote: On Wed, Aug 15, 2012 at 4:31 PM, Albert mailmd2...@gmail.com wrote: hello: Does anybody have any idea for the new version? when would it be reachable? and what's new? You can always try the current version of any of the branches using Git: http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage There you can access the latest versions of the 4.5, 4.6 and master branches. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] when?
On 8/15/12 11:09 AM, Albert wrote: hello: that's for kind reply. The unreleased version probably is not stable enough. I am asking for the official released version. As we can see the 4.5.5 is the one which was released almost one year ago. Do you have any idea when the next version would be officially released? And what's new comparing with current 4.5.5? A few details: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 http://www.gromacs.org/Documentation/Cut-off_schemes There is no scheduled release date. The new features and fixes are quite massive. There have been several delays, though many of the pending features are under review in the Gerrit system. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Dear David: If the two leaflets are moving with respect to each other (along the bilayer plane), then why would this be artificial? I have also seen this (diffusive) motion, and in addition to wondering why you would call it artificial, it seems to me that the motion would have to be many orders of magnitude larger than is observed in simulations for it to affect the temperature. Subtracting the COM of each leaflet separately is not only impossible, but inadvisable. Chris. -- original message -- I ran into similar issues for a DPPC bilayer. It might be possible that the two leaflets of the bilayer are moving with respect to eachother. If this is not taken into account, these artificial velocities will mean the simulation thinks it is at a higher temperature than it really is. If possible, you might want to try subtracting the center of mass motion of each leaflet, rather than the center of mass motion of the entire bilayer. This will allow the system to equillibrate to the correct (higher) temperature, and should increase the area per lipid of the bilayer. Hope this helps. -David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] PMF - Protein-Mebrane
The large magnitudes of orthogonal barriers in such systems will lead to both systematic and statistical sampling errors that motivate the application of both approaches, preferably repeated a few times each. So I think that Justin is right, in an idealized situation. I might modify his statement to indicate that the actual (converged) free energy is a state function, but the estimate of the free energy that you obtain from finite-time simulations may well depend on the methodological approach. Using multiple methodological approaches and initial conformations is a good way to ensure convergence or to identify sampling errors. Chris. -- original message -- I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane complex and pull out protein to separate them and calculate the PMF? What would be the difference? DeltaG is a state function; the direction is irrelevant. Keeping the sign consistent with the final and initial states is the only thing that really matters. -Justin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] my VMD
I suggest that you post this to the VMD users list. -- original message -- Dear All, I just installed a VMD. And then I load a gro file and a xtc file from a simulation. The bar in the VMD Main window continuously moves, however the protein molecule in the OpenGL Display window does not move. Will you please tell me what is the problem, or how can see the whole simulation? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
On 2012-08-14 08:52:26PM -0300, Sebastien Cote wrote: Dear Peter, I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as in Klauda's paper). I will retry with a more solvated membrane. Would you have any thought on how the NPAT ensemble might affect peptide-membrane interactions like I am studying i.e. peptide is totally solvated, then adsorb, and finally may insert? The paper on peptide-membrane interaction like this usually use united-atom lipid in the NPT ensemble. Most of the work I have seen on Charmm membrane in the NPAT ensemble were for embedded membrane protein. Sorry, but I only have experience with large pre-embedded membrane proteins, and those are governed both by signal sequences and post-translational modification. Chris's last email on the subject might lead to the hypothesis that lipid raft translation as the leaflets slide past one another could be a contributing factor to adsorbption of your species. Thanks, Sebastien Date: Mon, 13 Aug 2012 16:12:29 -0500 From: p...@uab.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Oh something I didn't mention: for bond constraints I used h-bonds instead of all-bonds. This may or may not make a difference (although I switched to h-bonds based on the suggestion of some charmm/lipid thread on here from a couple of years ago). On 2012-08-09 12:34:19PM -0300, Sebastien Cote wrote: Dear Peter, Did you use any different simulation conditions for your POPC membrane? I tried many different ones for POPE, without never reproducing Klauda's results. I may try yours on my POPE membrane. In my simulations, I want to study peptide-membrane interactions. The peptide is not embedded in the membrane. It is initially completely solvated without any interactions with the membrane. Then, I want to look at its adsorption and degree of insertion in the membrane. For that system, I can not remove the CoM motion of the protein alone, otherwise it will not adsorb and insert in the membrane. I may try (as you suggested) to remove CoM of the bottom leaflet on one hand, and the peptide-upperleaflet on the other hand. My peptide is not very long (17 to 35 amino acids), so I believe that remove the CoM of the peptide-upperleaflet/bottomleaflet will not have any pernicious effect. What do you think? Thanks for the suggestion, Sébastien Date: Wed, 8 Aug 2012 20:19:56 -0500 From: p...@uab.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Personally, I could remove the COM of each leaflet when equilibrating the bilayer by itself (and as a side note I am not experiencing a similar problem with POPC that you're having with POPE...). However, after the protein is embedded, I have gotten good results for my protein, which extends from the water through the entire membrane into more water, by using a whole System COM removal. The introduction of my particular embedded protein acts as a physical coupling between the water layers with the lipids (not to mention if I choose to model the lipid raft localization crosslink, it will have to happen anyway). If your protein doesn't extend fully past both layers of the membrane you may want to stick with just coupling a Membrane+Protein+1 layer of water or Membrane+Protein and Water separately (like in Justin's KALP15 tutorial). You will have to decide what you think is physically realistic based on the interaction between the water, membrane, and protein when the protein is embedded. (if your protein is assymetrically embedded you may even use the following COM groups: protein+involved leaflet, second leaflet, water). On 2012-08-09 09:38:01AM +1000, Mark Abraham wrote: On 9/08/2012 3:28 AM, Sebastien Cote wrote: Thanks for the suggestion. I tried it, but for my system the gain is not significant. I was aware that it is preferable to remove the centre-of-mass for each leaflet separately. However, in my tests, I removed the center-of-mass of the membrane because I intent to simulate peptide-membrane interactions. In such case, the center-of-mass of the protein-membrane system is usually removed. Is their any way to remove the CoM motion of each leaflet separately on one hand, and peptide-membrane system CoM motion on the other? See 7.3.3 of manual. Mark Thanks, Sebastien Date: Fri, 3 Aug 2012 11:10:22 -0400 Subject: Re: [gmx-users] CHARMM36 - Smaller
[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
The area per lipid (APL) will certainly affect the free energy of peptide/protein binding to a lipid bilayer. I have not used charmm lipids extensively, but from what I understand they older charmm lipids required NPAT to get the correct APL. The newer charmm lipids were supposed to solve that problem, but I have heard it said that, though the problem has been alleviated to some extend, it still remains. If I were you, I'd use POPC in place of POPE. POPE is notorious for giving too-small APL's in simulations and I think it even requires temperatures of 323 K to enter the liquid phase. That said, I don't have a specific answer to your question of whether there are other affects of NPAT vs. NPT. It is plausible that NPAT-based fluctuations could affect the pathway or the kinetics. PS: I was not referring to lipid rafts, but the separate diffusion of the upper and lower leaflets. Once the peptide is fully inserted, if it spans both leaflets, this will tend to reduce this leaflet-specific diffusion and would represent an entropic penalty for binding (not sure how large). Chris. Dear Peter, I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as in Klauda's paper). I will retry with a more solvated membrane. Would you have any thought on how the NPAT ensemble might affect peptide-membrane interactions like I am studying i.e. peptide is totally solvated, then adsorb, and finally may insert? The paper on peptide-membrane interaction like this usually use united-atom lipid in the NPT ensemble. Most of the work I have seen on Charmm membrane in the NPAT ensemble were for embedded membrane protein. Sorry, but I only have experience with large pre-embedded membrane proteins, and those are governed both by signal sequences and post-translational modification. Chris's last email on the subject might lead to the hypothesis that lipid raft translation as the leaflets slide past one another could be a contributing factor to adsorbption of your species. Thanks, Sebastien -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Thanks for the advices Chris. My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien From: chris.ne...@mail.utoronto.ca To: gmx-users@gromacs.org Date: Wed, 15 Aug 2012 17:29:29 + Subject: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? The area per lipid (APL) will certainly affect the free energy of peptide/protein binding to a lipid bilayer. I have not used charmm lipids extensively, but from what I understand they older charmm lipids required NPAT to get the correct APL. The newer charmm lipids were supposed to solve that problem, but I have heard it said that, though the problem has been alleviated to some extend, it still remains. If I were you, I'd use POPC in place of POPE. POPE is notorious for giving too-small APL's in simulations and I think it even requires temperatures of 323 K to enter the liquid phase. That said, I don't have a specific answer to your question of whether there are other affects of NPAT vs. NPT. It is plausible that NPAT-based fluctuations could affect the pathway or the kinetics. PS: I was not referring to lipid rafts, but the separate diffusion of the upper and lower leaflets. Once the peptide is fully inserted, if it spans both leaflets, this will tend to reduce this leaflet-specific diffusion and would represent an entropic penalty for binding (not sure how large). Chris. Dear Peter, I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as in Klauda's paper). I will retry with a more solvated membrane. Would you have any thought on how the NPAT ensemble might affect peptide-membrane interactions like I am studying i.e. peptide is totally solvated, then adsorb, and finally may insert? The paper on peptide-membrane interaction like this usually use united-atom lipid in the NPT ensemble. Most of the work I have seen on Charmm membrane in the NPAT ensemble were for embedded membrane protein. Sorry, but I only have experience with large pre-embedded membrane proteins, and those are governed both by signal sequences and post-translational modification. Chris's last email on the subject might lead to the hypothesis that lipid raft translation as the leaflets slide past one another could be a contributing factor to adsorbption of your species. Thanks, Sebastien -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Write the authors of the simulation paper that has a correct APL for POPE and ask them for an input file. That is really the only way to be sure that you are not doing something different than they did. In my experience, people are quite willing to provide you with their input file(s). If you still get a different APL than they reported, then see if your simulation times are similar and repeat your run a few times to see if it's just statistical noise. Regarding 323 K, I don't recall... it's just a number that sticks in my head. Perhaps it is for DPPE or DPPC. I'd still suggest that you at least try POPC. So your peptide binds more favourably to POPE than to POPC... that alone does not limit you to POPE. Then again, I don;t know exactly what you are trying to do. Chris. -- original message -- My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
On 2012-08-15 06:55:59PM +, Christopher Neale wrote: Write the authors of the simulation paper that has a correct APL for POPE and ask them for an input file. That is really the only way to be sure that you are not doing something different than they did. In my experience, people are quite willing to provide you with their input file(s). If you still get a different APL than they reported, then see if your simulation times are similar and repeat your run a few times to see if it's just statistical noise. The fundamental problem Sebastian will have is that Klauda obtained their APLs using CHARMM software, and he is trying to reproduce this using the forcefield in Gromacs software. So even if the CHARMM input files were provided, it maybe difficult to exactly reproduce the conditions in Gromacs (if certain parameters were implemented differently) Regarding 323 K, I don't recall... it's just a number that sticks in my head. Perhaps it is for DPPE or DPPC. I'd still suggest that you at least try POPC. So your peptide binds more favourably to POPE than to POPC... that alone does not limit you to POPE. Then again, I don;t know exactly what you are trying to do. Chris. It is generally a good idea to use a higher temp than the phase transition temperature, since during equilibration close to the phase transition temp there is a risk of inducing some ordering due to uneven heating. People run DPPC at 323 because its phase transition temp is 315K. If POPC's is 271 and people typically run POPC at 300, then it may be wise to bump up the running temp of a POPE system. Of course, your APL will inflate at higher temperatures... -- original message -- My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Hi, As I suggested earlier in this thread, I think the original poster should run test simulations of a CHARMM36 POPE membrane using either the NAMD or CHARMM softwares. It has been mentioned a couple of times in the thread thay there are differences in the implementations of the switching methods for the van der Waals interactions between softwares, and in my opinion this is one potential cause of the low area per lipid for the POPE membrane. This can be tested from these simulations in NAMD or CHARMM. Another potential explaination is that the relatively short simulation of Klauda et al. (40 ns) was not converged. As for other POPE force fields, the standard Berger parameters will not perform well. There are some force fields that have been reported to perform well. Apart from a couple of GROMOS ones I know of (GROMOS-CKP and GROMOS 43A1-S3 - I have used these in the past and both behave well at 313 K, which is well above the gel-liquid crystal phase transition temperature of 298 K), all-atom AMBER lipid parameters have been recently reported that include POPE (http://pubs.acs.org/doi/abs/10.1021/ct300342n). This may be another option that could be used for these simulations, with an AMBER force field used for the protein. Cheers Tom On 15/08/12 20:09, Peter C. Lai wrote: On 2012-08-15 06:55:59PM +, Christopher Neale wrote: Write the authors of the simulation paper that has a correct APL for POPE and ask them for an input file. That is really the only way to be sure that you are not doing something different than they did. In my experience, people are quite willing to provide you with their input file(s). If you still get a different APL than they reported, then see if your simulation times are similar and repeat your run a few times to see if it's just statistical noise. The fundamental problem Sebastian will have is that Klauda obtained their APLs using CHARMM software, and he is trying to reproduce this using the forcefield in Gromacs software. So even if the CHARMM input files were provided, it maybe difficult to exactly reproduce the conditions in Gromacs (if certain parameters were implemented differently) Regarding 323 K, I don't recall... it's just a number that sticks in my head. Perhaps it is for DPPE or DPPC. I'd still suggest that you at least try POPC. So your peptide binds more favourably to POPE than to POPC... that alone does not limit you to POPE. Then again, I don;t know exactly what you are trying to do. Chris. It is generally a good idea to use a higher temp than the phase transition temperature, since during equilibration close to the phase transition temp there is a risk of inducing some ordering due to uneven heating. People run DPPC at 323 because its phase transition temp is 315K. If POPC's is 271 and people typically run POPC at 300, then it may be wise to bump up the running temp of a POPE system. Of course, your APL will inflate at higher temperatures... -- original message -- My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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?
[gmx-users] box vectors - regd
Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Any help will be highly appreciated. Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Well, gromacs is not the only software available. I'd still ask them and then try it in gromacs after parsing. \If there is a difference, then try in NAMD and/or charmm. I know that this is the gromacs users list, but we're talking about debugging here and I think that getting the original parameter file and interpreting to gromacs or exactly rerunning in charmm is still the best way to go. If he can reproduce it in charmm, but not in gromacs, then the problem becomes more well defined. I stand by my advice. Chris. -- original message -- Peter C. Lai pcl at uab.edu Wed Aug 15 21:09:31 CEST 2012 Previous message: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Next message: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] On 2012-08-15 06:55:59PM +, Christopher Neale wrote: Write the authors of the simulation paper that has a correct APL for POPE and ask them for an input file. That is really the only way to be sure that you are not doing something different than they did. In my experience, people are quite willing to provide you with their input file(s). If you still get a different APL than they reported, then see if your simulation times are similar and repeat your run a few times to see if it's just statistical noise. The fundamental problem Sebastian will have is that Klauda obtained their APLs using CHARMM software, and he is trying to reproduce this using the forcefield in Gromacs software. So even if the CHARMM input files were provided, it maybe difficult to exactly reproduce the conditions in Gromacs (if certain parameters were implemented differently) Regarding 323 K, I don't recall... it's just a number that sticks in my head. Perhaps it is for DPPE or DPPC. I'd still suggest that you at least try POPC. So your peptide binds more favourably to POPE than to POPC... that alone does not limit you to POPE. Then again, I don;t know exactly what you are trying to do. Chris. It is generally a good idea to use a higher temp than the phase transition temperature, since during equilibration close to the phase transition temp there is a risk of inducing some ordering due to uneven heating. People run DPPC at 323 because its phase transition temp is 315K. If POPC's is 271 and people typically run POPC at 300, then it may be wise to bump up the running temp of a POPE system. Of course, your APL will inflate at higher temperatures... -- original message -- My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds exist at each timestep in my trajectory. My question is, how does the order of entries in the [ hbonds ] section in hbond.ndx relate to the order of entries in hbmap.xpm? I am running Gromacs 4.5.5. The man page for g_hbond_d clearly states: -hbm: existence matrix for all hydrogen bonds over all frames... . Ordering is identical to that in -hbn index file. However, I did a test of a system with two hydrogen bonds (which exist at different times), and it seems (although I am not at all certain) that the opposite is actually true. My hbond.ndx file contains the following section at the end of the file: [ hbonds ] 457458587 457458737 And my hbmap.xpm file indeed contains two entries (following the enumeration of x-axis values/times): ooo oo ooo oo o ooo oo o ooo oo o o oo, o o which tells me that one of the hydrogen bonds exists for a very large fraction of the trajectory, whereas the other exists for only two timesteps during the trajectory. I visualized the system in VMD. I clearly see that the hydrogen bond 457 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index file) is the one that exists for the vast majority of the trajectory. Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for only two timesteps in the trajectory. Based on this, it seems that the top-to-bottom order of hbmap.xpm is actually _opposite_ that of the [ hbonds ] section in hbond.ndx. Has anyone else tested this? If so, what conclusion did you reach about the ordering in the -hbn and -hbm output files. Or do you see a mistake in my reasoning above? One assumption I have made in my above reasoning is that o means the hydrogen bond exists, whereas means the hydrogen bond does NOT exist. I am not 100% sure that this is correct, but plotting the matrix as an EPS file using xpm2ps seems to say that I am correct. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
Hi again, I just looked at page 214 in the version 4.5.4 PDF manual (not the -h man page), and it says: An H-bond existence map can be generated of dimensions # H-bonds X # frames. The ordering is identical to the index file (see below), but reversed, meaning that the last triplet in the index file corresponds to the first row of the existence map. So this seems to answer my question. The order is indeed reversed. I do NOT mean this as a criticism, but just politely I would like to say that the -h man page for g_hbond may thus be a little vague and potentially misleading. Thanks, Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
On 8/15/12 4:49 PM, Andrew DeYoung wrote: Hi, I am a novice user of g_hbond (actually, I am using double precision -- g_hbond_d -- but I think all of the parameters should be the same). I would like to use the output of the -hbn switch (which generates hbond.ndx) in tandem with the -hbm switch (which generates an existence matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds exist at each timestep in my trajectory. My question is, how does the order of entries in the [ hbonds ] section in hbond.ndx relate to the order of entries in hbmap.xpm? I am running Gromacs 4.5.5. The man page for g_hbond_d clearly states: -hbm: existence matrix for all hydrogen bonds over all frames... . Ordering is identical to that in -hbn index file. However, I did a test of a system with two hydrogen bonds (which exist at different times), and it seems (although I am not at all certain) that the opposite is actually true. My hbond.ndx file contains the following section at the end of the file: [ hbonds ] 457458587 457458737 And my hbmap.xpm file indeed contains two entries (following the enumeration of x-axis values/times): ooo oo ooo oo o ooo oo o ooo oo o o oo, o o which tells me that one of the hydrogen bonds exists for a very large fraction of the trajectory, whereas the other exists for only two timesteps during the trajectory. I visualized the system in VMD. I clearly see that the hydrogen bond 457 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index file) is the one that exists for the vast majority of the trajectory. Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for only two timesteps in the trajectory. Based on this, it seems that the top-to-bottom order of hbmap.xpm is actually _opposite_ that of the [ hbonds ] section in hbond.ndx. Has anyone else tested this? If so, what conclusion did you reach about the ordering in the -hbn and -hbm output files. Or do you see a mistake in my reasoning above? One assumption I have made in my above reasoning is that o means the hydrogen bond exists, whereas means the hydrogen bond does NOT exist. I am not 100% sure that this is correct, but plotting the matrix as an EPS file using xpm2ps seems to say that I am correct. Your interpretation of the contents is correct. The first entry in hbonds.ndx is also the first entry in the .xpm file, which is the last line (index zero, hence the first entry). I have a script that calculates hydrogen bond existence time (plot_hbmapl.pl) from these two files if you want to confirm your outcome. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond
On 8/15/12 4:54 PM, Andrew DeYoung wrote: Hi again, I just looked at page 214 in the version 4.5.4 PDF manual (not the -h man page), and it says: An H-bond existence map can be generated of dimensions # H-bonds X # frames. The ordering is identical to the index file (see below), but reversed, meaning that the last triplet in the index file corresponds to the first row of the existence map. So this seems to answer my question. The order is indeed reversed. I do NOT mean this as a criticism, but just politely I would like to say that the -h man page for g_hbond may thus be a little vague and potentially misleading. We've had these discussions before on the list (several times). It may be a bit confusing at first, but if you think about the numbering of the y-axis in the .xpm file, it is numbered like any other, starting with the coordinate origin. Thus the values increase upward. To plot it backwards I think would be vastly more confusing, and each analysis program (g_hbond, do_dssp, g_mdmat, etc) would have to choose whether its output would be written forward or backward since they all share the same code for writing .xpm files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] box vectors - regd
On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] RE: Re: potential energy
Thanks for the reply Mark, I posted without thinking enough. In my workflow I have 10 ensembles. I sample one frame of co-ordinates per ps at the end of my NPT equilibration and generate new velocities for each of these frames. So they all have minor variations in initial position and velocity. My thinking was this would still allow system level deterministic effects to occur. Since I can't see a statistically significant difference in the interaction energy plots I was wondering if the ligand internal energies combined with the interaction energies might show the difference between runs with movement and those without. In the g_energy dialog I can get angle and dihedral forces for the whole system, but I can't see how to get those values for just one energy group (ligand in my case). A thought that just occurred to me, should I also be using LIG-LIG interactions as well as LIG-rest? All the best, Tom On 14/08/2012 11:07 AM, Tom Dupree wrote: Greetings all, Can I easily obtain the potential energy for a energy group rather than the whole simulation cell? Yes. See manual 3.3 and 7.3.8. But below you imply you're already doing this. You can make custom groups - see http://www.gromacs.org/Documentation/File_Formats/Index_File Does it make any sense to do so? Doubt it. I am simulating protein ligand complexes and have observed movement in some cases. When I analyse the interaction energy sum of LJ and columbic of LIG-rest (or Lig-Protein + Lig-rest) I get very flat energy plots with no significant differences between the runs where movement occurs and runs where it does not. I am wondering if there are some energy terms I have not accounted for that may explain the differences and thought potential energy may be one. However any changes in ligand potential energy are going to be dwarfed by protein and water changes. You can't expect to get an accurate quantitative picture by only looking at changes in internal energy, or only such changes for part of the system, because you have no estimate for how often those configurations arise. If the statistics from multiple runs of the same ensemble are significantly different, then you know you haven't converged any of the runs, and so probably can't say anything sensible about them. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] box vectors - regd
Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, if so how can i extract them. Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] box vectors - regd
On 16/08/2012 3:22 PM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs They're in the trajectory file with each frame. As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, Same. if so how can i extract them. Probably however you did so with NAMD, or with g_traj or gmxdump. Mark Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
