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 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. ________________________________ From: [email protected] [mailto:[email protected]] On Behalf Of Pablo Umazano Sent: Thursday, 19 March 2009 10:19 AM To: [email protected] 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 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. Thank. Pablo
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