[gmx-users] Required help in topology making
Dear All I have a protein where one residue ( Lysine ) is making a covalent bond with the cofactor Pyridoxal phosphate. I have created other parameters of heteroatom PLP through PRODRG and manual checking. But I am not sure how to include the parameters for the imine bond ( C=N bond ) that has been formed between side chain amine group of lysine and aldehyde group of Pyridoxal phosphate. Do I have to edit C-termini database file ( ff-c.tdb ) ? A clue to this problem will be highly appreciated. Regards Supti Mukhopadhyay Senior Research Fellow Department of Psychopharmacology NIMHANS, Bangalore India ___ 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] question about continuation using tpbconv and mdrun -cpi
Hi Mark, Thanks! Because the maximum time for one single job is set to be 24hours on the cluster I'm using, I want to make sure which is the best way to continue the gmx jobs. I wonder how strong effect mdrun -cpi has? From the introduction of mdrun, it seems that there are some EXTRA energy frames, but for the trajectory file (.xtc), there is no extra frames? Am I right? mdrun -h -- The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). best wishes, Mark Abraham wrote: Baofu Qiao wrote: Hi all, Recently I made some tests on the continuation of gmx 4.0.5. Firstly, I run a complete simulation as the reference. In the full.mdp file, gen_seed=123456 continuation=yes are used to build the same initial structure. In all the simulations, mdrun -dlb no is used because I want to reproduce exactly the same potential energy. 1. Using tpbconv. (part1.mdp is the same as full.mdp except the nsteps) 1a) grompp -s part1 mpirun -np 32 mdrun -deffnm part1 -dlb no tpbconv -s part1.tpr -f part1.trr -e part1.edr -extend 100 -o part2 mpirun -np 32 mdrun -deffnm part2 -dlb no eneconv -f part1.edr part2.edr -o part_all.edr 1b) tpbconv -s part1.tpr -extend 100 -o part2.tpr mpirun -np 32 mdrun -deffnm part2 -cpi part1.cpt -dlb no eneconv -f part1.edr part2.edr -o part_all.edr The potential energy is generated from g_energy, and compared. In this method, I met two problems: Q.a) The potential energies of part2 in both 1a and 1b are not exactly the same as the reference potential! And also the potential of part2 in 1a is different from that in 1b. (Both potentials of part1 from 1a and 1b are identical to the reference.) Q.b) The RMSD of the potential energies of part_all.edr is very big (1 order of magnitude bigger than the corresponding one from the separate .edr files) 2) using mdrun -cpi -append grompp -s full2 mpirun -np 32 mdrun -deffnm full2 -dlb no (stop the job at some time point, then run the following) mpirun -np 32 mdrun -deffnm full2 -dlb no -cpi full2_prev.cpt -append The second (-append) section of the potential energy is also different from the result of the reference potential, even though I am using the same full.mdp file. (the potential in the former section is identical to the reference) Then, how to reproduce exactly the potential? While mdrun -dlb no is a good start, mdrun -reprod takes care of some other things too... It is said that the continuation from mdrun -cpi is binary identical. Not quite... it's an exact restart from the old point in the ensemble, but the manner in which mdrun does future integration is only reproducible if you force it to be so. However, it seems not in my tests. What's the problem of the very big RMSD of the potential from eneconv? Not sure. 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 ___ 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] Required help in topology making
supti mukherjee wrote: Dear All I have a protein where one residue ( Lysine ) is making a covalent bond with the cofactor Pyridoxal phosphate. I have created other parameters of heteroatom PLP through PRODRG and manual checking. But I am not sure how to include the parameters for the imine bond ( C=N bond ) that has been formed between side chain amine group of lysine and aldehyde group of Pyridoxal phosphate. Do I have to edit C-termini database file ( ff-c.tdb ) ? No, that's only useful for tweaking things along the peptide backbone. Simplest, if you already know what you are doing, is to edit the .rtp file to make a modified lysine residue that has the cofactor with all the right parameters. Then pdb2gmx can just work on a structure you provide that has the cofactor. Detailed knowledge of chapter 5 of the manual will be required. As a guide, you might construct a cofactor-bound lysine, and give that to PRODRG and use the topology generated as a partial template for the modified lysine residue. Perhaps work on a H2C=N lysine modification first of all, and then scale up. Whether PRODRG generates suitable parameters is something you will have to verify independently. 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] question about continuation using tpbconv and mdrun -cpi
Baofu Qiao wrote: Hi Mark, Thanks! Because the maximum time for one single job is set to be 24hours on the cluster I'm using, I want to make sure which is the best way to continue the gmx jobs. I wonder how strong effect mdrun -cpi has? From the introduction of mdrun, it seems that there are some EXTRA energy frames, but for the trajectory file (.xtc), there is no extra frames? Am I right? mdrun -h -- The contents will be binary identical (unless you use dynamic load balancing), but for technical reasons there might be some extra energy frames when using checkpointing (necessary for restarts without appending). The intent with GROMACS 4.x is for a user to be able to construct a .tpr with a very long simulation time, and perhaps constrain mdrun with -maxh (or rely on the cluster killing the job), and to use the information in the checkpoint file to restart correctly and perhaps to then use mdrun -append so that when the simulation is running smoothly, only one set of files needs to exist. Thus one doesn't need to trouble with using tpbconv correctly, crashes can restart transparently, etc. The old-style approach still works, however. Obviously you should (be able to) verify with mdrun -reprod that whatever approach you use when you construct your job scripts leads to simulations that are in principle reproducible. For production, don't use -reprod because you will want the better speed from dynamic load balancing, etc. 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
[gmx-users] How to fi all atoms and to calculate the energy
Is it posible to calculate the energy of a protein without to execute any steps of MD ? I need to claculate the initla enregy but wihtout excute stesp of dynamic. How do I fix all atoms of a protein in Gromacs ? Thanks best regards -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional ___ 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 fi all atoms and to calculate the energy
Is it posible to calculate the energy of a protein without to execute any steps of MD ? I need to claculate the initla enregy but wihtout excute stesp of dynamic. How do I fix all atoms of a protein in Gromacs ? Hasn't that been answered a few days ago!? just run a zero step md simulation. the energy of the system (possibly tour protein) will be written in the log file. you do not need to fix the protein atoms ... they won't move since you do not run an md .. Thanks best regards -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional ___ 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] How to fi all atoms and to calculate the energy
XAvier Periole wrote: Is it posible to calculate the energy of a protein without to execute any steps of MD ? I need to claculate the initla enregy but wihtout excute stesp of dynamic. How do I fix all atoms of a protein in Gromacs ? Hasn't that been answered a few days ago!? just run a zero step md simulation. the energy of the system (possibly tour protein) will be written in the log file. you do not need to fix the protein atoms ... they won't move since you do not run an md .. Yes, it was asked a few days ago, and I answered about the same thing. 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] Re: mdrun -nosum still complains that 15 % of the runtime was spent communicating energies
chris.ne...@utoronto.ca wrote: Perhaps assigning the result of this to a variable and printing it before executing it would help confirm that -nosum really was there. I am not sure what you mean... the while line as a variable? I'm pretty sure that -nosum is there. I meant to suggest including in the script command=mpirun mdrun -youroptions print $command `$command` or similar. Then the output can tell you what the state of the environment was when the command was issued, which can help you troubleshoot things. 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
[gmx-users] infinite surface
Hello everybody. I am a Gromacs beginner, so sorry if this question is trivial and/or I am not precise. I would like to simulate an infinite surface of graphene (or any other planar lattice structure). Gromacs supports pbc also in two directions (as far as I understood) and that would really be perfect for my purposes but.. in order to have a periodic infinite lattice, I need to have atoms on one face of the cell being connected to the atoms on the opposite face. So, how can I do this? Just by modifying the CONNECT section of the input .pdb file? Will gmx programs understand? J Thank you in advance! Regards Giulio ___ 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 fi all atoms and to calculate the energy
Hi Luis, If you want only the initial energy, you can try minimize your system using gradient conjugate (cg) or steepest descent (steep) algorithm with large value of tolerance (emtol). Of course, using steeps of MD from GROMACS. I hope this help. Ph.D. Osmair V. Oliveira Federal University of Sao Carlos Brazil Date: Wed, 29 Jul 2009 08:22:38 -0300 From: luis.sc...@ufabc.edu.br To: gmx-users@gromacs.org Subject: [gmx-users] How to fi all atoms and to calculate the energy Is it posible to calculate the energy of a protein without to execute any steps of MD ? I need to claculate the initla enregy but wihtout excute stesp of dynamic. How do I fix all atoms of a protein in Gromacs ? Thanks best regards -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional _ Com o Windows Live, você pode organizar, editar e compartilhar suas fotos. http://www.microsoft.com/brasil/windows/windowslive/products/photo-gallery-edit.aspx___ 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] infinite surface
Giulio Scocchi wrote: Hello everybody. I am a Gromacs beginner, so sorry if this question is trivial and/or I am not precise. I would like to simulate an infinite surface of graphene (or any other planar lattice structure). Gromacs supports pbc also in two directions (as far as I understood) and that would really be perfect for my purposes but.. in order to have a periodic infinite lattice, I need to have atoms on one face of the cell being connected to the atoms on the opposite face. So, how can I do this? Just by modifying the CONNECT section of the input .pdb file? Will gmx programs understand? J No, GROMACS ignores CONNECT sections. Check out the advice here. http://oldwiki.gromacs.org/index.php/Carbon_Nanotube 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
[gmx-users] Re: openmm
As I found out by testerror myself, mdrun-openmm will not work with systems with more than one chain. Cheers, Alan On Tue, Jul 28, 2009 at 15:04, Alan alanwil...@gmail.com wrote: Dear all, Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac and Windows so far, and it comes with examples, pretty neat. Even though there's some apparently fixes compared to the usual release of openmm and gromacs-openmm, my molecule didn't work with it yet. Nevertheless, for those with nvidia cuda and Mac or Windows, it's worth trying. Cheers, Alan On Sat, Jul 18, 2009 at 18:31, Alan alanwil...@gmail.com wrote: Thanks Justin. I could swear I tried what you said... anyway it worked now (2.5 x faster), but not with implicit solvent for mdrun-openmm... Trying with plain mdrun with the setup for implicit solvent and it seemed to work (although I don't know how to interpret this from GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: even though this is not available in the standard Gromacs 4) I still would like an example/tutorial that really worked for someone with gmx openmm. In the end, with mdrun-openmm and implicit solvent in the mdp file, I got a file md.gro full of nan nan. For those interested, here are the commands I did. If you have GMX with ffamber, CUDA and GMX-openmm you may reproduce it. ### cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = Reaction-Field ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step epsilon_rf = 0 pbc = no EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no comm_mode = ANGULAR ; uncomment below to test with implicit solvent ;implicit_solvent = GBSA ;gb_algorithm = OBC ;gb_epsilon_solvent = 78.3 EOF wget -c http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdbcompression=NOstructureId=1BVG -O 1BVG.pdb grep 'ATOM ' 1BVG.pdb| Protein.pdb grep 'HETATM' 1BVG.pdb| Ligand.pdb sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \ | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \ | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \ | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g | ProteinAmber.pdb # Process with pdb2gmx and define water pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -ignh grompp -f em.mdp -c Protein2.pdb -p Protein.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr # OK mdrun-openmm -v -deffnm md # 3 times fater # works fine without set for implicit solvent in md.mdp # with implicit solvent, md.gro full of nan nan nan everywhere. ### On Sat, Jul 18, 2009 at 17:31, Alanalanwil...@gmail.com wrote: Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp? ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented My full md.mdp file is: integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no implicit_solvent = GBSA
Re: [gmx-users] Re: openmm
Alan wrote: As I found out by testerror myself, mdrun-openmm will not work with systems with more than one chain. Please contact the authors with this sort of feedback for them to put in their documentation. I'm not aware that they subscribe to this list. 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
[gmx-users] -append on jugene overwrites trr
Hello all together, in my compilation of Gromacs 4.0.5 on JUGENE (a Blue Gene/P machine in Jülich), the -append option does not work properly. When i restart a simulation from a checkpoint, the mdrun recognizes the checkpoint and -append (one can see it in md.log), but instead of appending to md.log, traj.trr, ener.edr, it overwrites them. The file offsets in state.cpt (printed by gmxdump -cp) are shown here: number of output files = 3 output filename = md.log file_offset_high = 0 file_offset_low = 21265 output filename = traj.trr file_offset_high = 0 file_offset_low = 9021240 output filename = ener.edr file_offset_high = 0 file_offset_low = 5872 The same distribution compiled for JUMP (a Power6 machine running under AIX) works correctly. Details to the machines can be found here http://www.fz-juelich.de/jsc/service/sco_ibmBGP http://www.fz-juelich.de/jsc/service/sco_ibmP6 Does anybody know how to solve/work around? At the moment i have to store continuations of a simulation run into different directories, which complicates analysing data, e.g. the calculation of time-dependent properties for the whole run. Many thanks in advance for any hints! Leonid ___ 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] -append on jugene overwrites trr
Dr. Leonid Yelash wrote: Hello all together, in my compilation of Gromacs 4.0.5 on JUGENE (a Blue Gene/P machine in Jülich), the -append option does not work properly. Possibly that's intrinsic to the way I/O is handled on BlueGene. It should be simple to create a test program that tries to append to an existing file. Mark When i restart a simulation from a checkpoint, the mdrun recognizes the checkpoint and -append (one can see it in md.log), but instead of appending to md.log, traj.trr, ener.edr, it overwrites them. The file offsets in state.cpt (printed by gmxdump -cp) are shown here: number of output files = 3 output filename = md.log file_offset_high = 0 file_offset_low = 21265 output filename = traj.trr file_offset_high = 0 file_offset_low = 9021240 output filename = ener.edr file_offset_high = 0 file_offset_low = 5872 The same distribution compiled for JUMP (a Power6 machine running under AIX) works correctly. Details to the machines can be found here http://www.fz-juelich.de/jsc/service/sco_ibmBGP http://www.fz-juelich.de/jsc/service/sco_ibmP6 Does anybody know how to solve/work around? At the moment i have to store continuations of a simulation run into different directories, which complicates analysing data, e.g. the calculation of time-dependent properties for the whole run. Many thanks in advance for any hints! Leonid ___ 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] -append on jugene overwrites trr
Hi, I don't know if you know eneconv and trjcat, these programs can merge your output. So you can still do all your analysis. Berk Date: Wed, 29 Jul 2009 23:48:36 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] -append on jugene overwrites trr Dr. Leonid Yelash wrote: Hello all together, in my compilation of Gromacs 4.0.5 on JUGENE (a Blue Gene/P machine in Jülich), the -append option does not work properly. Possibly that's intrinsic to the way I/O is handled on BlueGene. It should be simple to create a test program that tries to append to an existing file. Mark When i restart a simulation from a checkpoint, the mdrun recognizes the checkpoint and -append (one can see it in md.log), but instead of appending to md.log, traj.trr, ener.edr, it overwrites them. The file offsets in state.cpt (printed by gmxdump -cp) are shown here: number of output files = 3 output filename = md.log file_offset_high = 0 file_offset_low = 21265 output filename = traj.trr file_offset_high = 0 file_offset_low = 9021240 output filename = ener.edr file_offset_high = 0 file_offset_low = 5872 The same distribution compiled for JUMP (a Power6 machine running under AIX) works correctly. Details to the machines can be found here http://www.fz-juelich.de/jsc/service/sco_ibmBGP http://www.fz-juelich.de/jsc/service/sco_ibmP6 Does anybody know how to solve/work around? At the moment i have to store continuations of a simulation run into different directories, which complicates analysing data, e.g. the calculation of time-dependent properties for the whole run. Many thanks in advance for any hints! Leonid ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] about mdrun_make_hole.tar.gz
Dear all, I want to insert a protein (L-shaped) in lipid bilayer whose C-terminal segment remains trans-membrane with solvent exposed N-terminus. For that reason, i want to use make_hole program. I have downloaded mdrun_make_hole.tar.gz gromacs-3.1.4.tar.gz from the new gromacs homepage. But when i try to uncompress mdrun_make_hole.tar.gz using gunzip or tar -zxvf, the file seems to be corrupted. From the old gromacs homepage this file can not be downloaded. Can anyone provide me the mdrun_make_hole.tar.gz file. 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
RE: [gmx-users] infinite surface
List, Regarding tutorials and tubes. Is/ are their any tutorials that describe how to form a tube, and then add a molecular system within the tube that flows in one end and out the other, continuously? Thanks. Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, July 29, 2009 7:51 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] infinite surface Giulio Scocchi wrote: Hello everybody. I am a Gromacs beginner, so sorry if this question is trivial and/or I am not precise. I would like to simulate an infinite surface of graphene (or any other planar lattice structure). Gromacs supports pbc also in two directions (as far as I understood) and that would really be perfect for my purposes but.. in order to have a periodic infinite lattice, I need to have atoms on one face of the cell being connected to the atoms on the opposite face. So, how can I do this? Just by modifying the CONNECT section of the input .pdb file? Will gmx programs understand? J No, GROMACS ignores CONNECT sections. Check out the advice here. http://oldwiki.gromacs.org/index.php/Carbon_Nanotube 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 ___ 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: openmm
Dear Mark, I've contacted the authors already. I decided to publish here as well just to close this topic. Alan On Wed, Jul 29, 2009 at 13:45, Alan alanwil...@gmail.com wrote: As I found out by testerror myself, mdrun-openmm will not work with systems with more than one chain. Cheers, Alan On Tue, Jul 28, 2009 at 15:04, Alan alanwil...@gmail.com wrote: Dear all, Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac and Windows so far, and it comes with examples, pretty neat. Even though there's some apparently fixes compared to the usual release of openmm and gromacs-openmm, my molecule didn't work with it yet. Nevertheless, for those with nvidia cuda and Mac or Windows, it's worth trying. Cheers, Alan On Sat, Jul 18, 2009 at 18:31, Alan alanwil...@gmail.com wrote: Thanks Justin. I could swear I tried what you said... anyway it worked now (2.5 x faster), but not with implicit solvent for mdrun-openmm... Trying with plain mdrun with the setup for implicit solvent and it seemed to work (although I don't know how to interpret this from GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: even though this is not available in the standard Gromacs 4) I still would like an example/tutorial that really worked for someone with gmx openmm. In the end, with mdrun-openmm and implicit solvent in the mdp file, I got a file md.gro full of nan nan. For those interested, here are the commands I did. If you have GMX with ffamber, CUDA and GMX-openmm you may reproduce it. ### cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = Reaction-Field ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step epsilon_rf = 0 pbc = no EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no comm_mode = ANGULAR ; uncomment below to test with implicit solvent ;implicit_solvent = GBSA ;gb_algorithm = OBC ;gb_epsilon_solvent = 78.3 EOF wget -c http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdbcompression=NOstructureId=1BVG -O 1BVG.pdb grep 'ATOM ' 1BVG.pdb| Protein.pdb grep 'HETATM' 1BVG.pdb| Ligand.pdb sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \ | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \ | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \ | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g | ProteinAmber.pdb # Process with pdb2gmx and define water pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -ignh grompp -f em.mdp -c Protein2.pdb -p Protein.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr # OK mdrun-openmm -v -deffnm md # 3 times fater # works fine without set for implicit solvent in md.mdp # with implicit solvent, md.gro full of nan nan nan everywhere. ### On Sat, Jul 18, 2009 at 17:31, Alanalanwil...@gmail.com wrote: Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp? ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented My full md.mdp file is: integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no
[gmx-users] Solvation Implicit
Hi, How do I do to claculate a MD with implict solvation in the Gromacs ? Thanks -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional ___ 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] Creation of a tube and then simulating molecular flow through it.
List, Regarding tutorials and tubes. Is/ are their any tutorials that describe how to form a tube, and then add a molecular system within the tube that flows in one end and out the other, continuously? Thanks. Jim ___ 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] Users software contribution. Old site.
Hi, I can't download the software form the users contributions section located on the old gromacs website (http://oldwww.gromacs.org/component/option,com_docman/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,35/). As pressing download it seems to open binary file in the browser window instead of downloading it. I cannot find the analogous section on the new site as well. How is it possible to access these data now? Thanks, Vitaly ___ 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 change the protonation state of an aminoacid in a peptide
Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing the protonated state for this residue? Thanks in advance -- Camilo Andrés Jiménez Cruz ___ 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 change the protonation state of an aminoacid in a peptide
Camilo Andrés Jimenez Cruz wrote: Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing the protonated state for this residue? Well, the command that you entered should have worked (it always has for me). As for getting any extra advice, you will have to provide a much more complete description, including the following: 1. Which force field you are trying to use 2. Relevant output (from screen and from the structure/topology) 3. Which Gromacs version you are using 4. Any relevant details on compiler types, computer system, and how Gromacs was compiled -Jusitn Thanks in advance -- 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] Users software contribution. Old site.
Vitaly V. Chaban wrote: Hi, I can't download the software form the users contributions section located on the old gromacs website (http://oldwww.gromacs.org/component/option,com_docman/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,35/). As pressing download it seems to open binary file in the browser window instead of downloading it. I cannot find the analogous section on the new site as well. How is it possible to access these data now? The new site seems to be working for me thus far: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software -Justin Thanks, Vitaly ___ 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 -- 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] Solvation Implicit
Luis Paulo wrote: Hi, How do I do to claculate a MD with implict solvation in the Gromacs ? Implicit solvent will be officially implemented in version 4.1; I believe some progress has been made in the development versions, but a developer would have to comment on its functionality. -Justin Thanks -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- 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] How to change the protonation state of an aminoacid in a peptide
I already found the problem, Thanks! The point is that I was using a non standard forcefield, In this forcefield, the protonated state is called ASH. the program tried to find the ASPH and as it couldn't it didn't changed anything. Thanks again! On Wed, Jul 29, 2009 at 4:53 PM, Justin A. Lemkuljalem...@vt.edu wrote: Camilo Andrés Jimenez Cruz wrote: Hi. I have the gro file for a peptide in vacuum, in the peptide, there is only one ASP, and I want to change it to ASPH. If I run pdb2gmx -asp and select the protonated state, the only change is in the name of the residue (it doesn't add the needed hydrogen). Is there any automatic way changing the protonated state for this residue? Well, the command that you entered should have worked (it always has for me). As for getting any extra advice, you will have to provide a much more complete description, including the following: 1. Which force field you are trying to use 2. Relevant output (from screen and from the structure/topology) 3. Which Gromacs version you are using 4. Any relevant details on compiler types, computer system, and how Gromacs was compiled -Jusitn Thanks in advance -- 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 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 -- Camilo Andrés Jiménez Cruz ___ 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] with dispersion correction ...
Dear all, I am simulation spc water system in NVE ensemble. During the grompp stage, it gave me 2 Notes that rlist should be 0.1-0.3 nm bigger than rcolumb and rvdw. So I chose rlist=0.9 and two others=0.7 also another Note told me that I use vdwtye=shift and columbtype=PME-switch. That solved the problem in this stage, however, in the mdrun step, I got a Fatal error: - Program mdrun, Version 4.0.5 Source code file: sim_util.c, line 842 Fatal error: With dispersion correction rvdw-swith can not be zero for vdw-type=shift. --- Any idea about it and what value I should use for rvdw-swith ?? Thank You in advance, Jamie ___ 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] with dispersion correction ...
Jamie Seyed wrote: Dear all, I am simulation spc water system in NVE ensemble. During the grompp stage, it gave me 2 Notes that rlist should be 0.1-0.3 nm bigger than rcolumb and rvdw. So I chose rlist=0.9 and two others=0.7 also another Note told me that I use vdwtye=shift and columbtype=PME-switch. That solved the problem in this stage, however, in the mdrun step, I got a Fatal error: - Program mdrun, Version 4.0.5 Source code file: sim_util.c, line 842 Fatal error: With dispersion correction rvdw-swith can not be zero for vdw-type=shift. --- Any idea about it and what value I should use for rvdw-swith ?? This is usually given in the literature: Lennard-Jones interactions were shifted to zero smoothly between [rvdw-switch] and [rvdw]. I don't know any force field for which a 0.7-nm vdW cutoff is really appropriate; most were parameterized with longer cutoffs. I suggest looking into values designed for whatever force field you are using, and whether or not such a treatment of vdW terms is appropriate. -Justin Thank You in advance, Jamie ___ 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 -- 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
[gmx-users] Pulling a CG protein
Dear gromacs users, Hi, I am trying to pull apart a relatively large protein (CG using the martini force field) by pulling on two groups in opposite directions. To do this, I will be using the following .mdp file. However, I am almost certain that it contains errors: title= Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 17000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2500 nstvout = 2500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect the general performance of ; the model. ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; MARTINI - normal temperature and pressure coupling schemes ; can be used. It is recommended to couple individual groups ; in your system seperately. ; Temperature coupling = tcoupl = V-Rescale ; Groups to couple separately = tc-grps = PROTEIN W ; Time constant (ps) and reference temperature (K) = tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 3.0 compressibility = 3e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 323 gen_seed = 666 ; OPTIONS FOR BONDS = ; MARTINI - for ring systems constraints are defined ; which are best handled using Lincs. constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 60 ; FREEZE GROUP ; Pulling pull= afm pull_geometry = direction pull_start = no pull_nstxout= 10 pull_nstfout= 10 pull_ngroups= 2 pull_group0 = pull_group1 = pull pull_vec1 = -0.1764 -0.9823 -0.0625 pull_init1 = -0.1764 -0.9823 -0.0625 pull_rate1 = 0.0001 pull_k1 = 1000 pull_group2 = freeze pull_vec2 = 0.1764 0.9823 0.0625 pull_init2 = 0.1764 0.9823 0.0625 pull_rate2 = 0.01 pull_k2 = 5000 The reason why group 2 has such a high force constant and low pull rate is because I wanted to simulate putting a harmonic constraint on the freeze group. However, when I process this .mdp with grompp, I get the following message: WARNING 1 [file md_vinculin.mdp, line unknown]: Unknown or double left-hand 'pull_group2' in parameter file WARNING 2 [file md_vinculin.mdp, line unknown]: Unknown or double
Re: [gmx-users] How to Run Energy Minimisation
Nancy wrote: Hello, I am trying to run energy minimisation on a lipid bilayer (downloaded from: http://moose.bio.ucalgary.ca/files/dppc128.pdb). I inflated the bilayer using InflateGRO however, when I try to run the minimisation, it seems to display the un-inflated bilayer. Please advise. Without seeing the command lines that you're issuing, we can only assume you are doing something wrong. -Justin Thank you. Nancy ___ 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 -- 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] How to Run Energy Minimisation
Hello, More specifically, I am unsure as to the procedure of inflating and minimizing a bilayer using InflateGRO. In the tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I followed it successfully up to the inflation step, but I do not know specifically what parameters to run the energy minimisation. Please advise. Thank you. Nancy On Wed, Jul 29, 2009 at 7:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Nancy wrote: Hello, I am trying to run energy minimisation on a lipid bilayer (downloaded from: http://moose.bio.ucalgary.ca/files/dppc128.pdb). I inflated the bilayer using InflateGRO however, when I try to run the minimisation, it seems to display the un-inflated bilayer. Please advise. Without seeing the command lines that you're issuing, we can only assume you are doing something wrong. -Justin Thank you. Nancy ___ 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 -- 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 ___ 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 Run Energy Minimisation
Nancy wrote: Hello, More specifically, I am unsure as to the procedure of inflating and minimizing a bilayer using InflateGRO. In the tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I followed it successfully up to the inflation step, but I do not know specifically what parameters to run the energy minimisation. Please advise. Most general EM .mdp files are suitable; a simple one is linked in Step 1 on the page you quote above, Orient the protein and membrane; modifications that should be made to it are described in Step 2, Pack the lipids around the protein. The caveat to my membrane protein tutorial was that the user should already be used to normal input/output routines with Gromacs. A simpler tutorial to familiarize you with Gromacs procedures can be found at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html It might be useful if you are unfamiliar with simulation protocols with Gromacs, since it is conceptually easier and more detailed in the description of each step. If the minimized bilayer is not showing up as inflated, then you probably invoked InflateGRO incorrectly (hence why I asked for the command lines you invoked). Usage is described in the text of the inflategro.pl script, and I describe typical scaling factors that should be used for the procedure in the tutorial. -Justin Thank you. Nancy On Wed, Jul 29, 2009 at 7:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Nancy wrote: Hello, I am trying to run energy minimisation on a lipid bilayer (downloaded from: http://moose.bio.ucalgary.ca/files/dppc128.pdb). I inflated the bilayer using InflateGRO however, when I try to run the minimisation, it seems to display the un-inflated bilayer. Please advise. Without seeing the command lines that you're issuing, we can only assume you are doing something wrong. -Justin Thank you. Nancy ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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
[gmx-users] Re: Users software contribution. Old site.
Thanks, Justin. I succeeded eventually with your link. Vitaly On Wed, Jul 29, 2009 at 11:54 PM, Justin A. Lemkuljalem...@vt.edu wrote: Vitaly V. Chaban wrote: Hi, I can't download the software form the users contributions section located on the old gromacs website (http://oldwww.gromacs.org/component/option,com_docman/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,35/). As pressing download it seems to open binary file in the browser window instead of downloading it. I cannot find the analogous section on the new site as well. How is it possible to access these data now? The new site seems to be working for me thus far: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software -Justin Thanks, Vitaly ___ 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 -- 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 -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, cell.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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
