Re: [gmx-users] Boundary
On 7/6/12 3:06 PM, dariush wrote: Hi all, Why does GROMACS just provide PBC for boundary condition? However, LAMPPS as an example provides four kind of boundary: periodic, non-periodic and fixed, non-periodic and shrink-wrapped and non-periodic and shrink-wrapped with a minimum value. Gromacs can also do non-periodic systems by setting "pbc = no" in the .mdp file. A variety of options exist for walls, as well. If there are particular features that users want, they are welcome to implement them and submit them for review in the development code. Otherwise, if no one files a feature request on redmine, the developers aren't going to invest time in the feature unless they need it themselves. I would hazard a guess that 3-D periodic boundary conditions are the most commonly used in simulations of biomolecules. PBC makes problem when you want to make movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Any trajectory can be "fixed" for visualization purposes with trjconv. You may need several iterations to achieve the desired effect. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Boundary
Hi all, Why does GROMACS just provide PBC for boundary condition? However, LAMPPS as an example provides four kind of boundary: periodic, non-periodic and fixed, non-periodic and shrink-wrapped and non-periodic and shrink-wrapped with a minimum value. PBC makes problem when you want to make movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/Boundary-tp4999167.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] boundary conditions
Use position constraints? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] boundary conditions
Hi, I've a DNA molecule, and I want to simulate MD when the DNA has an extremity fixed. So I have to block some degree of freedom. How could I do this? thanks Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
