I am trying to run a Radial Distribution Function (RDF) trajectory analysis between water (WAT) hydrogen atoms and ligand (UNN) nitrogen atoms using the production trajectory (prod1.crd) and the parameter file (solvated.prmtop).
When i use the rdf.in file as;
parm solvated.prmtop
trajin prod1.crd
radial rdf.xmgr 0.1 15.0 :WAT@H:UNN@N
The calculation ends in less than 1 second, and no output file gets generated.
However, if I modify the rdf.in to;
parm solvated.prmtop
trajin prod1.crd
trajout rdf.xmgr
radial rdf.xmgr 0.1 15.0 :WAT@H:UNN@N
and run the analysis using "cpptraj rdf.in", it starts to generate an output file (rdf.xmgr) that is 60+ Gb in size which cannot be read using xmgrace (Column count incorrect) as it seems to be an coordinates file (picture enclosed).
Will you please help me troubleshoot the cause and find a proper solution?
It is a simple question that you have added the wrong command line:
trajout rdf.xmgr
. Remove it!
It is a simple question that you have added the wrong command line:
trajout rdf.xmgr
. Remove it!
Thank you very much for your highly appreciated answer.
Actually, when I do not use "trajout" the calculations generates no output at all. It just finishes within ~1 second while no output at all.
I managed to solve it. I think (but not completely sure) that was because of the partial incompatibility between Amber 18 and AmberTools 20. I managed to do it with the help of AmberTools 19, since it is compatible with Amber 18.
Again, your answer is highly appreciated.
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