Hello, since I am also need direct access to the forces and play around a little bit I realized that this is not that easy. However if you set "nstfout=1", you should get the forces in every step.But I have another question, regarding the direct part of the coulomb forces.
Since we have worked out an error estimation for the SPME algorithm, that allows us to estimate the absolute error introduced by the interpolation and the cutoff. We wrote a little tool to test the estimate and it works very well. But comparing the forces calculated by this tool and Gromacs yields a root mean square difference of the forces of 10^-4. That is a very big difference, because the precision of the forces should be 10^-12. Now the question arises, which forces are "wrong" ? Since I talk about the forces of the first step before any integration, only the force calculation can introduce the differences and I can not imagine, that the compiler optimizations are responsible. Moreover the comparison was done, using the Ewald sum, so there is no FFT involved, that can cause the differences. The next point I thought about were the tabulated potentials, but turning this of in the source code yielded even a larger difference.
The problem is that the error estimate of Kolafa and Perram ( http://dx.doi.org/10.1080/08927029208049126 ) for the Ewald sum underestimates the error introduced by Gromacs, while our tool fits to the estimate. Can anybody imagine the source of difference ? Furthermore I have found no possiblity to turn of the tabulation of the coulombic forces in the mdp options, did I miss it or is there no possibility ? Finally it would be very interested in a possiblity to switch off the vdw interactions easily. So far I used an appropiate topology files with C6 and C12 set to zero. Is there an easier solution as using a table filled with zeros ? Cheers, Flo * Mark Abraham <[email protected]> [2009-01-06 08:45:05 +1100]:
Silvia Crivelli wrote:Hello, I need to calculate the forces (derivatives) for every atom in a protein as this is being locally minimized using mdrun.When I run mdrun I can get the maximum force F-max and the atom on which thisforce is evaluated printed in the log file (for example, "F-max = 2.20323e+03 on atom 2641 ".) I need to be able to compute the force value on every atom of the protein. How can I do this with Gromacs?I set the parameter nstfout = 10 in my .mdp file but this doesn't seem to make a difference.
"nstfout = 10" writes the per-atom forces to the trajectory file every 10 steps, which you can verify with gmxcheck and/or gmxdump. I haven't verified that these actually get written for energy minimization, and they probably wouldn't get written at all if your EM doesn't get to 10 steps....Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected].Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Computational and Theoretical Softmatter & Biophysics group Frankfurt Institute for Advanced Studies Johann-Wolfgang-Goethe University Ruth-Moufang-Str. 1 60438 Frankfurt am Main Phone: +49(0)69 / 798 - 47529 Fax: +49(0)69 / 798 - 47611 EMail: [email protected] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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