output file of mdrun_openmm have all value 0

[vinod jani]

hello,
I was able to compile and install openmm version of gromacs Now when I am running all the values in md.log are 0.I am using Amber99 force field.


Thanks
Vinod Jani

[vinod jani]

hello,
I was able to compile and install openmm version of gromacs Now when I am running all the values in md.log are 0 . I am using Amber99 force field.what could be probable reason for this ?

Thanks

[Mark Friedrichs]

What board are you running on? What values in the log file are 0? Perhaps you can send me your tpr file (friedrim@stanford.edu), and I can try running it here to see if we can reproduce the problem.

[Peter Eastman]

We don't currently report energies correctly, so any energies in the log will be zero.

Peter

[Mark Friedrichs]

Hi Jani,

From the md.log file you sent, it appears the simulation ran fine, except that the 'params.agb' file was not being found and so the implicit solvent portion of the calculation was not included -- that file needs to be copied to the Gromacs 'share/gromacs/top/' directory. The line in the log file is
'Could not open file=</usr/local/gromacs/share/gromacs/top/params.agb>. Could not read agb file. GBSA is being omitted.'

I have emailed you a compressed tar file w/ the results obtained here. You can check if your run is doing something by either visually viewing the trajectory using a tool like VMD or using the Gromacs utility 'gmxdump' to generate an ASCII file of the trr file contents; this will allow you to confirm that the coordinates, ... are being updated.

Mark

[vinod jani]

Dear Mark,
Thanks for help,
But even after copying the params.agb file the values remained zero.And even when i am running g_energy_openmm it giving error Energy file md_ener.edr not recognized, maybe different CPU?
Trajectory file seems to be ok.
So for purpose of analysis which file we have to look as log file have all values zero.

[Peter Eastman]

I already said: we do not currently record energies, so all of them will be zero.

Peter