[gmx-users] problem with force fields while running membrane protein simulation
Dear all and Justin... I am trying to do membrane protein simulation by following justin's tutorial using gromacs 4.5.3 version. I selected ffG53a6 force field and pasted the content of lipid.itp file to the corresponding files as per the instructions in the tutorial but i got error (Fatal error: Atomtype CA not found) while running grompp command. I tried some other options by selecting different forcefields but the problem persist. I think gromacs is not accepting the file after modifications. Please kindly help me in this regard... -- Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] problem with force fields while running membrane protein simulation
On 4/02/2011 7:54 PM, Mohana lakshmi wrote: Dear all and Justin... I am trying to do membrane protein simulation by following justin's tutorial using gromacs 4.5.3 version. I selected ffG53a6 force field and pasted the content of lipid.itp file to the corresponding files as per the instructions in the tutorial but i got error (Fatal error: Atomtype CA not found) while running grompp command. I tried some other options by selecting different forcefields but the problem persist. I think gromacs is not accepting the file after modifications. Please kindly help me in this regard... Don't try force fields randomly. You will normally be able to use one of a very few possibilities, and preferably exactly the right one. I can only suppose you haven't followed Justin's tutorial instructions closely enough. 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/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] problem with force fields while running membrane protein simulation
Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. -- Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] problem with force fields while running membrane protein simulation
On 4/02/2011 9:00 PM, Mohana lakshmi wrote: Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. Please leave the context for the discussion in subsequent emails. You can better remember the context of your problem than us because it is more important to you than it is to us :-) Perhaps the tutorial is not updated for more recent GROMACS versions. Perhaps you aren't using the right environment to access your multiple versions of GROMACS (e.g. re-sourcing GMXRC from the other location(s)). 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/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] problem with force fields while running membrane protein simulation
Thank you Mark. Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] what standard is successful when doing EM
Hi, guys Water molecule starting at atom 10578 can not be settled. Check for bad contacts and/or reduce the timestep. When i run 6x6x1.3nm water box. i used several methods to do EM. So i can do several EM. But which .gro should i select as my input .gro for my running？ Because when i use different .gro, i got different results. So here i thought there should be a standard. Please note, Even when the Max-force is below 50, there will also be different .gro structure. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] what standard is successful when doing EM
On 4/02/2011 10:07 PM, gromacs wrote: Hi, guys Water molecule starting at atom 10578 can not be settled. Check for bad contacts and/or reduce the timestep. When i run 6x6x1.3nm water box. i used several methods to do EM. So i can do several EM. But which .gro should i select as my input .gro for my running?? Because when i use different .gro, i got different results. So here i thought there should be a standard. Please note, Even when the Max-force is below 50, there will also be different .gro structure. Yes, that's very normal. Potential energy surfaces of proteins are very rough. Small differences in EM algorithms find different minima or regions of minimas. Life's too short to be worried about finding the lowest one. The usual purpose of EM is to relieve bad contacts before starting equilibration. As such, anything after EM that's rather better than what you started with is normally OK. So if equilibration succeeds, you probably did fine with EM. If not, do some detective work. 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/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] problem with force fields while running membrane protein simulation
Mark Abraham wrote: On 4/02/2011 9:00 PM, Mohana lakshmi wrote: Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. The tutorial is not compatible with version 3.3.3, based on the commands. The expectations regarding Gromacs version are explained in the tutorial's first page. Please leave the context for the discussion in subsequent emails. You can better remember the context of your problem than us because it is more important to you than it is to us :-) Perhaps the tutorial is not updated for more recent GROMACS versions. Perhaps you aren't using the right environment to access your multiple versions of GROMACS (e.g. re-sourcing GMXRC from the other location(s)). As far as the tutorial, it is up-to-date with instructions for 4.0.x (principally) and 4.5.x (via some side notes). The problem the OP is having is from not following directions closely enough. CA is a Gromos87 atomtype, being called from the lipid.itp nonbonded section. Proper removal of incompatible parameters and subsequent extension of Gromos96 is one of the central features of the tutorial. -Justin Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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: Energy calculation problem with molecule leaving the box
I extracted trajectories with -pbc center -mol to obtain ones with molecules that form different energy groups in all combinations and then rerunned the simulation. This procedure was described here http://lists.gromacs.org/pipermail/gmx-users/2007-October/030104.html I seem to get a reasonable interaction energy throughout the simulation and no zeroes. Is this a good procedure to calculate interaction energy? The reason why I am doing energy calculations posteriori is that a solvent molecule enters the calixarene cavity but I don't know which one is doing that until after the simulation. --- Begin Message --- On 4/02/2011 1:05 AM, Gordan Horvat wrote: I'm doing molecule dynamics of a calixarene in a acetonitrile box with pbc, energy groups defined and npT constant. When I extract interaction energies with g_energy from edr file I expect them to be pretty much constant because I see no significant conformational changes or changes in distance between energy groups and that is true for one part of simulation when the molecule is completely in the box. But when a molecule partially leaves the box energies of interaction for that part which is out of the is box is not calculated (bonded or with other energy groups) and interaction energy sometimes drops to 0.000 for a period of time even though the distance between groups doesn't change. I tried extracting energies through rerunning simulation on trajectories which were converted with -pbc nojump or -pbc mol -center but that gave zero energies all the time. How can I fix this energy calculation problem? So, having run your original simulation with pre-defined energy groups, starting from the mdrun output files, what commands reproduce your observations? Mark --- End Message --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Error Messages
Hi, I run GROMACS in parallel mode. The first two jobs that I submitted are still running. However, when I tried to submit the third job, and stopped for the following reason: Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 1.025 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition What does the error message mean? Thanks for your help. Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Error Messages
simon sham wrote: Hi, I run GROMACS in parallel mode. The first two jobs that I submitted are still running. However, when I tried to submit the third job, and stopped for the following reason: Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 1.025 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition What does the error message mean? http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm -Justin Thanks for your help. Best, Simon Sham -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] harmonic restraint with OpenMM
Hi, I am trying to restrain an ion that is coordinated by a few protein atoms, to avoid that the ion might fly off. The simulation should be run on a GPU (with OpenMM) and implicit solvent. First I tried to restrain the ion using bonds of type 6, but harmonic potentials are not supported by OpenMM. Turning the restraint into a normal bond (type 1) would be fine since I only constrain bond lengths of hydrogens. However, that gives a grompp error, "Cannot find length for atoms 386-2262 involved in angle" meaning that the function find_gb_bondlength in topio.c does not find a bond length for the ion-protein atom bond, although the bond length is clearly defined in the topology. I am a bit stuck now. Does anyone know how one could introduce some kind of distance restraint with OpenMM and implicit solvent? I am using gmx 4.5.3 and OpenMM 2.0. Thanks a lot, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell& Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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
