Re: [gmx-users] Continuation diferent machine.

Binary identical means that the files are identical bit-for-bit, i.e. if you ran "cmp traj1.trr traj2.trr" it would report the files to be the same/indistinguishable. This is normally only important for debugging. If you don't know it doesn't apply to you :-) All that matters for you is t

[gmx-users] editconf and the placement of the center of mass

Hi, In editconf, there's an option -center which allows you to place the geometrical center of your molecular at a desired location. I was wondering, is there an analogous option for the placement of the center of mass of a molecule? Thanks, Arneh __

Re: [gmx-users] Continuation diferent machine.

Hi Erick, Thank you for you responce. I am sorry but I dont unterstand the term "_binary_ identical results". The first simulation was run on a linux machine (pentium 4) with gromacs 3.2 from the rpm included in suse. The new machine will be (Pentium4 Xeon) with gromacs 3.3 (manual compiled)

Re: [gmx-users] Continuation diferent machine.

Hi Anthony, As long as the version you're continuing with is the same or more recent than the one you started with it should work fine; all gromacs output files are stored in portable formats and are can be read by newer versions. You are not guaranteed _binary_ identical results, though

[gmx-users] Continuation diferent machine.

Hi users: I have made some simulation in one of our workstation. Now I want to extend the simulations few nanoseconds. I can continue the simulations in other machine without affecting the results? I need to use the same gromacs version? Best Regards, Anthony __

RE: [gmx-users] Timestep

Ramya, A timestep of dt=0.002 already means a timestep of 2fs, since the unit of dt is ps. So a timestep of dt=0.002=2 fs works fine for you, which is perfectly normal. If you want to go higher you need to use certain tricks, as suggested by Xavier. I suggest you read the manual (e.g. http://www.

Re: [gmx-users] Timestep

Hi, In principle Gromacs should never just crash with a segmentation fault, but at least give you a (perhaps cryptic) error message and exit somewhat gracefully. As far as I know there is only one exception to this: If you are using tabulated interactions the table can only be of finite s

Re: [gmx-users] Timestep

It is not possible to answer your question from the information you give. A lot of things can cause a segmentation fault. From compilation to your particular system. Put a search on the user-list, you'll get an idea of possible problems. It depends what you will be looking at but I would suggest

[gmx-users] Timestep

Hello.. Thanks to Xavier for his prompt reply.. Actually my objective is a bit longer[50-60ns] but the problem is that even if i cant change the time-step to 0.003 it is exiting saying segmentation fault then how is it possible with 1fs [or 4 fs as suggested] which i want to do to reduce tim

[gmx-users] Article gallery

Hi, Just to let you guys know, the 'article gallery' on the gromacs website doesn't seem to work anymore. mzzls Jeroen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

Re: [gmx-users] Timestep

10 ns of a solvated protein of regular size should not require much computing time. Increasing the time-step above 2 fs is a solution to increase the speed of the run but then you face the problem of not integrating the fast movement correctly and this can end up in large forces and then you run

Re: [gmx-users] how to run parallel jobs in gromacs

Did you booted your lam? Go to a specific node of your cluster, for example node 3, and create a file with a simple name like lamhosts. This file must contain just the nodes you may want to boot (the name of the node, like no3, or something like this). Than, run lamboot lamhosts -v If you have tw

[gmx-users] Timestep

Hello, I am trying to perform a simulation run of 10ns for my system [protein+waterbox].The system works fine if i use timestep[dt=0.002 fs]. To balance the run time and time-consumption, when we try a .mdp file with slight increase of timestep i.e., to 0.003 fs; grompp works fine and gener

Re: [gmx-users] Re:mdrun_problem

pkmukher wrote: Hi users, I am having a problem during the running of the mdrun program on my prepared system.I have a system containing a protein/peptide complex. i have prepared the protein using the pdb2gmx utility and the peptide using the PRODRG utility. I have then included the ligand .itp

[gmx-users] Mutagenesis

Hi everyone, I am new to mutagenesis studies, so I was wondering if I could get some input on my approach. My task involves mutagenizing a residue (with all 19 possibilities) in a protein that binds DNA, and then deciding whether the resulting structure is physically acceptable. My approach to d