[gmx-users] Re: Membrane Simulation

ete editconf command was "editconf -f protein.gro -o proetin.newbox.gro -box 12 12 12 -center 6 6 8.75 -rotate 145 -45 55" and to decrease the scaling factor from 4 to 2, but it was useless. I'm sorry to bother you so much, but I'm stucked with my project. Thank you so much.

[gmx-users] Re: Membrane Simulation

rocessed.gro -o protein_newbox.gro -c -box 6.23910 6.17970 6.91950 -rotate 85 -10 55 -center 8 8 6". Thanks for your patience and your appreciated help. Yours sincerely, GIuseppe -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Simulation-tp5007421p500744

[gmx-users] Membrane Simulation

so any help is much appreciated. Thanks a lot, GIuseppe Cimicata -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Simulation-tp5007421.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@g

Re: [gmx-users] CONSTRAINED SIMULATIONS

ee it work I decided to do NVT simulations. However, the problem persists. I'm using angle restraints on the "pulled" group in order to preserve its orientation with respect to the reference group. Could this be the problem? Cheers, Giuseppe 2010/1/24 > Dear Giuseppe: >

Re: [gmx-users] CONSTRAINED SIMULATIONS

-77.586782 1500.000122 -58.386616 Cheers, Giuseppe 2010/1/24 > Dear Giuseppe: > > *** What I am looking for is raw -pd pull.pdo data from the first run. > *** > > It looks like you did not define a name for -pd: > > mpiexec -n $NSLOTS mdrun_mp

Re: [gmx-users] CONSTRAINED SIMULATIONS

ce of constraints, in nm constraint_tolerance = 1e-06 Thank you for your patience. Giuseppe PS: I used the correct files to start the run again and I also visualized the configurations: thus, the pulled protein has moved for real (while it should be stuck at the initial point!). 2010/1/24 &

Re: [gmx-users] CONSTRAINED SIMULATIONS

Initializing reference group. Inv. mass: 0.70 Initial coordinates center of mass:2.9763.0058.828 Constraining the starting coordinates (step -2). Let me know what you think, thanks. Giuseppe 2010/1/24 > Please provide actual gromacs output and tell us where it is from. I know >

[gmx-users] CONSTRAINED SIMULATIONS

Hello, I'm trying to do constrained simulations of a system consisting of two solvated proteins separated at a given distance. Inside the box there are also around 14.000 water molecules. At the bottom there is the .pdo file (I'm using gromacs 3.3.3). However, it seems as it does not work. At the