[gmx-users] CHARMM and FEP calculations

Hi I asked a similar question a year ago about implementing CMAP in FEP calculations for gromacs 4.5.4. At the time I could not get the simulation to run with CMAP as it came up with: Fatal error: > Function type CMAP Dih. not implemented in ip_pert Helpfully, Mark suggested a modification to t

Re: [gmx-users] Pulling multiple groups

Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and it works- I think it might b

[gmx-users] Pulling multiple groups

Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull= constraint pull_geomet

[gmx-users] REMD output

Dear all, I want to double check, the output from an REMD simulation with Gromacs is the trajectory at constant Temp and whe you demux it with demux.pl, this is the trajectory of the replica which starts at a given tempurature and how it evolves through time? For instance, if _0.tpr file corres

[gmx-users] CMAP Dihedrals and free energy perturbations

Hi I was wondering if anyone could help me. I am trying to use Gromacs 4.5.4 to do some free energy calculations. I am using the CHARMM forcefield with CMAP and keep getting the error message: Fatal error: Function type CMAP Dih. not implemented in ip_pert I noticed that someone had posted a