Re: [gmx-users] Smooth surface
On Tuesday 07 November 2006 08:46, David van der Spoel wrote: Tsjerk Wassenaar wrote: Hi Alex, I think you're best off describing the wall with particles. You can freeze them to a specific position (make it a freeze-group) and set all interactions between them to zero. You can tune your particles to be hydrophilic or hydrophobic. Hope it helps, If that really is not what you want, then please write down some equations how you would treat a hydrophilic wall. Just a Lennard Jones is not very complicated, and we have actually done something like that in the past (Wensink et al. Langmuir 16 (2000), p. 7392). I need Lennard-Jones interactions in Z direction between walls and Oxygens of water molecules. And second, repulsion function (also in Z direction) between atoms of peptides and walls. I think that it is possible to introduce periodic boundary conditions only in x and y directions? -- Alex Krukau Physical Chemistry II a University Dortmund tel: + 49 231 755 3938 fax: + 49 231 755 3937 ___ 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
Re: [gmx-users] Smooth surface
Hi Alex, I think you're best off describing the wall with particles. You can freeze them to a specific position (make it a freeze-group) and set all interactions between them to zero. You can tune your particles to be hydrophilic or hydrophobic. Hope it helps, Tsjerk On 11/7/06, Alexei Krukau [EMAIL PROTECTED] wrote: On Tuesday 07 November 2006 01:41, Mark Abraham wrote: Alexei Krukau wrote: Dear Gromacs users, I would like to ask, if there is a possibility to create a smooth (unstructured) hydrophobic or hydrophilic wall in Gromacs? I think not, but it is hard for me to guess what you are trying to do. If you explain more clearly, other people may be better able to help you. Mark ___ 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 I would like to make a slit-like smooth pore, to calculate adsorption of some small peptides from liquid water on the pore walls. Hydrophilicity or hydrophobicity of the walls should be tunable. -- Alex Krukau Physical Chemistry II a University of Dortmund ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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
Re: [gmx-users] Smooth surface
Tsjerk Wassenaar wrote: Hi Alex, I think you're best off describing the wall with particles. You can freeze them to a specific position (make it a freeze-group) and set all interactions between them to zero. You can tune your particles to be hydrophilic or hydrophobic. Hope it helps, If that really is not what you want, then please write down some equations how you would treat a hydrophilic wall. Just a Lennard Jones is not very complicated, and we have actually done something like that in the past (Wensink et al. Langmuir 16 (2000), p. 7392). -- 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 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
