Re: [gmx-users] genbox problem with micelle
If you have the center coordinates and your cell has a good radial symmetry, i would just write a script, checking the distance of each water to the center and then skipping everything below the radius of your cell. Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
Re: [gmx-users] genbox problem with micelle
Alif M Latif wrote: Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p Thanks 4 reading...any comments and suggestion will be greatly appreciated.. A third alternative would be to increase the vdw radii, by copying vdwradii.dat to your working directory and increase the water radius. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] genbox problem with micelle
Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p Thanks 4 reading...any comments and suggestion will be greatly appreciated.. Alif Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
Re: [gmx-users] genbox problem with micelle
Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p genbox just uses vdw radii for different atom types to generate volumes that exclude waters. If your micelle (and I presume from the above that you have a micelle that is lipid-inside-surface water-outside-surface) has interstices that are large enough to admit waters, then genbox will place them there. Probably, an energy minimization of the micelle in vacuo will see it contract so that the lipids are pretty much close-packed, and hopefully this density will also be close to that for the micelle in solution. Alternatively, or if there are still holes that admit waters, you can make the radii of your lipid C and H atoms larger for the purposes of genbox using a modified gromacs/share/top/vdwradii.dat. Be careful later with the gentleness of your minimization and equilibration schemes else you'll generate large structural changes and thus bad contacts and LINCS errors, etc. Otherwise, you could get out a molecule visualization program like VMD, find the waters inside and delete them (you could script this with VMD, too). There's also a lesson here to look at your structure before you simulate to see that it looks how you expect it to. If you'd seen these waters, and knew for some reason that it would take longer than your simulation time to form an equilibrated micelle by excluding these waters, then you'd have known not to bother with this simulation, and fixed your problem without spending computer time needlessly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
