RMSD gives -nan (Plumed-2.0.1; Gromacs-4.6.5)

[Suman Chakrabarty]

Hello,

I am having a strange problem while trying to use the RMSD CV. My input file is:

RMSD REFERENCE=test.pdb TYPE=SIMPLE LABEL=d1

PRINT ARG=d1 STRIDE=1 FILE=COLVAR

... and I am using the "driver" option to calculate the RMSD as follows:

plumed driver --igro test.gro --plumed=plumed_driver.dat

... where test.gro and test.pdb have identical coordinates (apart from the units being different in these two formats), so the RMSD should be exactly zero. But, the generated COLVAR file contains the following:

#! FIELDS time d1

 0.000000 -nan

I get this "nan" for all RMSD calculations, even while running metadynamics with Gromacs, which crashes of course due to this "nan" issue.

Is there any known problem regarding this? How should I troubleshoot?

Thanks and regards,

Suman.

[Giovanni Bussi]

Hi,

can you post your PDB file?

Did you specify the weights correctly in the test.pdb file (beta and occupancy column)?

See http://plumed.github.io/doc-v2.0/user-doc/html/_r_m_s_d.html

Giovanni

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[Suman Chakrabarty]

Dear Giovanni,

Thanks! You have guessed correctly. The Beta column was zero in my PDB file. I should have read the documentation properly before trying it out! :)

Can you please clarify the need to use two separate sets of weights for COM and distance calculations? There is already one example of protein-ligand system specified in the manual. But in general one should put just the atomic masses in both the columns, right?

Another question: Is the PBC for distance calculations taken care of automatically during a metadynamics run (within Gromacs)? Or is it generally advised to use the WHOLEMOLECULES directive? Thanks.

Best regards,

Suman.

==============================================
Dr. Suman Chakrabarty
Ramanujan Fellow
Physical and Materials Chemistry Division
National Chemical Laboratory
Pune, 411008, India
Phone: +91-20-2590 3053
Web: www.namusite.com
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The true delight is in the finding out rather than in the knowing.
-- Isaac Asimov
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