[gmx-users] ACE - NME caps

Dear Gromacs users, I would like to use the ACE and NME (or NAC) caps for the NH and CO termini of a peptide, but unfortunately in charmm27 ff these groups do not exist. Although, in the file aminoacids.hdb there is the notation ACE. Also, in gromos43a1 and gromos53a6 ffs only the parameters fo

[gmx-users] mdrun_mpi -rerun bonded interactions

Dear GRomacs users, I am using the -rerun option of mdrun to read the coordinates of a trajectory and to compute the potential energy of a molecule during MD. This operation when performed in parallel, using mdrun_mpi, the energy of the bonded interactions is not computed. But using one core,

[gmx-users] Edit on-the-fly topology files (stateA->stateB)

Greetings GrOmAcS Users, I want to calculate the free energy, for different (de)protonation states, of a certain compound. This requires to edit by hand many topology files. Is there a code that can do it on-the-fly or any ideas(algorithm) how it can be done automatically? Thanks in advance f

[gmx-users] mdrun -rerun (not reproducible energy values?)

Dear Gromacs Users, I am using the -rerun option of mdrun to re-analyze a trajectory. Thus, I tried to rerun the same trajectory (md.xtc) with exactly the same md.tpr.  But the bonded interactions are not computed or written to the log file or to the .edr file, resulting to completely different

[gmx-users] maybe you are out of quota?

Dear Gromacs Users, The following error messages appear while running MD simulations with Gromacs 4.5.4: - Cannot flush logfile - maybe you are out of quota? - XTC error - maybe you are out of quota? - Cannot read/write checkpoint; corrupt file, or maybe you are out of quota? - Cannot write tr

[gmx-users] Estimation of free energy using Linear Response method

Dear Gromacs Users, I would like to ask how the Linear Response method can be applied for the calculation of free energy using the Gromacs package? More specifically, I am interested in the set-up of the MD protocol and the parameters of the input files. Thanks in advance for your help-- gmx-