[gmx-users] g_rdf program

Pablo Umazano pumazano at exactas.unlpam.edu.ar
Thu Mar 19 00:19:12 CET 2009

Hello, I am relatively new to gromacs and I really would appreciate help with the following question.


I have used a coarse-grained model to represent a DNA fragment with approximately 50 nm of length. I have run a Langevin dynamics simulation of DNA with ions NA+ and CL- to study their distribution of around DNA. During simulation I used the option to remove the center of mass motion (default option) because when there are no external forces the com linear moment must be conserved.

Now, I want study the redistribution of ions around DNA when an external electric field is applied. My doubt is the following: when external electric field is applied, should I remove the center of mass motion? I thought that the answer was no, then I tried the following option:


comm_mode    none


but half of DNA goes out of the box during simulation (I see this with ngmx and in out.gro) and nothing enters the another side.

I know gromacs use pbc to calculate the interactions between particles, but I wonder if g_rdf program considers that part of DNA is out the box to calculate the radial function distribution of ions around DNA.



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