Re: [gmx-users] Why density increase with increasing the cutoff length?

Would it be all cut-offs: elect + vdW ? Or the increase is separate? For your info the vdW are attractive potentials at long distances so an increase of cutoff would result in an increase of attraction and therefore to an increase of density! This is one good illustration of the fact that you s

Re: [gmx-users] Why density increase with increasing the cutoff length?

On 12/21/09 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there

[gmx-users] Why density increase with increasing the cutoff length?

Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me

[gmx-users] [Fwd: Gromacs podcast is out]

For your entertainmet during the holiday season, here are links to a podcast about GROMACS' past, present and future. Brock Palen and Jeff Squyres chat with me about GROMACS. Enjoy. http://www.rce-cast.com/index.php/Podcast/rce-23-gromacs.html The RSS feed for the show is: http://www.rce-c

Re: [gmx-users] How to calculate PN vector head group angle...

Henry Yang wrote: Hello gromacs experts, I want to calculate the PN vector angular distribution along the bilayer axis. I am currently using gromacs 4.0.5 version. Is there any tools in gromacs which one I can use to calculate this properties? If not, anyone pls tell me how can I proceed? I a

[gmx-users] How to calculate PN vector head group angle...

Hello gromacs experts, I want to calculate the PN vector angular distribution along the bilayer axis. I am currently using gromacs 4.0.5 version. Is there any tools in gromacs which one I can use to calculate this properties? If not, anyone pls tell me how can I proceed? I am actually quiet new

Re: [gmx-users] exert of special pH

leila karami wrote: Hi How I exert my favorite PH in simulation of pr-dna interaction in mdp file? And also special concentration of some salts. The concept of pH is not one that can be easily defined in a normal MD simulation. Please see the extensive discussion here: http://www.gr

[gmx-users] exert of special pH

Hi How I exert my favorite PH in simulation of pr-dna interaction in mdp file? And also special concentration of some salts. Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] Principal axis (g_principal)

Dear gmx users, I am doing several analyses (version 4.0.4) on my simulations with small organic molecules inserting into a DMPC bilayer. Now I would like to calculate whether the small molecule inserts into the membrane with a specific angle to the membrane normal (or z-axis). I have used two