[gmx-users] NVT conserved-energy lysozyme

Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling therm

[gmx-users] zn finger simulation

Dear allI am trying to run a simulation of a dimer including a zinc finger using Gromacs 4.5.3. I have gone through the documentation and searched the forums but could not find a specific answer to my problem. In order to produce the initial topology (top) and coordinate (gro) files for the sim

[gmx-users] issue with nsteps

Dear all I am having a problem with a Gromacs run that I have prepared for a total of 1e10 steps (actually nsteps=100; this accounts in this case for a total run time of 10 microseconds). When I run "grompp" I see in the preprocessing output that apparently the correct number of steps h

[gmx-users] Restarts: Truncation of file *.xtc failed

Dear Gromacs users I am experiencing a problem with restarts in a REMD simulation with explicit solvent in Gromacs 4.0.5. I am trying to continue a set of simulations that finished after the maximum time in our cluster queue had been reached. Therefore I just directly (i.e. without modifying my inp

[gmx-users] Re: Restarts: Truncation of file *.xtc failed

Hi Thanks Greg for your answer. Yes, my simulation is in fact pretty long and its files are considerably large. The size of the xtc files is approximately ~2 GB when I am trying to do the restart. I thought on the contrary that my problem was related to another post in today's list ( http://lists.g