[gmx-users] part number in extending simulation

2011-08-27 Thread Hsin-Lin Chiang
Hi, Is part number in extending simulation in ver.4.5.4 cancelled? Below is my shell script, #!/bin/bash a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md #running GROMACS /stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \ -nt 12 \ -s ${a}/md100ns.tpr \ -o ${a}/md100ns.trr \ -e ${a}/md100ns.edr \

[gmx-users] cannot inactivate fitting in g_rmsf - incomplete coordinates are written

2011-08-27 Thread Thomas Evangelidis
Dear GROMACS community, I am trying to calculate B-factors of a sample equilibrated system (31 frames). My trajectory is in .psf and .dcd format but I have created a .tpr file for my analysis from the first frame . First I eliminated random translation and rotation of my protein by fitting every f

Re: [gmx-users] termini modification

2011-08-27 Thread Justin A. Lemkul
lina wrote: pdb2gmx -ter I doubt this is of any use; the Amber force fields don't use the same conventional termini selection that the other force fields do, as the OP states. I suspect that's why the .tdb approach is not working. I think the best approach is to simply write .rtp entrie

Re: [gmx-users] termini modification

2011-08-27 Thread lina
pdb2gmx -ter On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj wrote: > Hello, > > I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the > terminal residues from NALA and CALA to normal ALA (just as middle > residues). As the terminal selection option is not enabled with the amber > ff,

[gmx-users] termini modification

2011-08-27 Thread Vijayaraj
Hello, I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the terminal residues from NALA and CALA to normal ALA (just as middle residues). As the terminal selection option is not enabled with the amber ff, I am using the termini modification parameters with aminoacids.c.tdb. here

[gmx-users] proper dihedral types in the topology

2011-08-27 Thread ZHANG Lu
Dear man or madam, I have a question about the dihedral types in the topology. If I made the topology by hand, is it possible to combine the type 9 and type 3 for proper dihedrals? Any comment about that? Thanks. Best, Lu -- gmx-users mailing listgmx-users@gromacs.org http://lists.g