[gmx-users] g_rdf program

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Mar 19 03:41:12 CET 2009

No, the molecule has not gone out the side of the box and not entered
the other side.  If you check the solvent on the opposite side of the
box, you will notice that there is a big hole that exactly matches up
with the DNA fragment that is sticking out.  Use the pbc options in VMD
to display neighbouring images of the box, that will make it much more
explicit what is going on.
Unless otherwise noted, the analsysis programs and intelligent enough to
realise where things are located.
Remember, with a periodic box, all things are relative.  The location of
the boundaries of the base unit are totally arbitary, you can move them
around at your will to visualise, it makes no difference to how things
are calculated or handled by the software.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 



	From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pablo Umazano
	Sent: Thursday, 19 March 2009 10:19 AM
	To: gmx-users at gromacs.org
	Subject: [gmx-users] g_rdf program
	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


	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




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