[gmx-users] t-coupling and freeze groups
Hi gmx-users, I have a small question about the temperature set of the freeze groups. Does it make sense to set it to 0K for freeze groups, if not, how does it influence on the rest of systems? Thanks in advance. ___ 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] position restraints with npt ensemble
Hi gmx-users, I want to restrain some atoms of a certain protein in water for production, but I am not sure whether it makes sense to make NPT simulations with position restraints. I mean if the coordinates of the restrained atoms are not scaled, it would be problematic in pressure coupling. Thanks in advance. ___ 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] question about anisotropic pressure couping
Hi all, I want to simulate a monoclinic crystal with a=0.52 nm, b=1.1 nm, c=2.1 nm and alpha=gama=0, beta=95.6 degree, so I construct a triclinic box. When I do a NPT simulation, I need the 6 components of compressibility as xx, yy, zz, xy, xz, yz, according to the manual. I have already get the three linear compressibility coefficients parallel to the unit cell edges as B_a, B_b, B_c, but I am not sure how to convert them to the format that gromacs needs. Any tips will be helpful. Thanks in advance. ___ 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] AFM Pulling and com motion
Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each other. There are really some distinct differences between them during the 80ps simulation. I worry about it, for example, in long time simulations, so I want to know which one is the better and reliable choice, stopcm or without stopcm. As I know, the NAMD package only removes the initial center of mass motion. Thanks for your reply. Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! This depends on what type of pulling you are doing. If you have an absolute reference you are right. But when you pull between two groups of atoms, there are no external forces, but internal forces between two groups. Berk. ___ 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] AFM Pulling and com motion
Thanks for your reply. There is no absolute reference here. The system is just from this web site http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007; (hands-on: The pull package). I really do not know the advantage or necessity of stopcm in SMD, because when I test the two systems, with and without stopcm, there is a distinct difference between the calculated pull force. You didn't tell if you are using an absolute reference or not. With an absolute reference you should not remove the com motion. Berk. From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 22:44:29 +0800 Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each other. There are really some distinct differences between them during the 80ps simulation. I worry about it, for example, in long time simulations, so I want to know which one is the better and reliable choice, stopcm or without stopcm. As I know, the NAMD package only removes the initial center of mass motion. Thanks for your reply. Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! This depends on what type of pulling you are doing. If you have an absolute reference you are right. But when you pull between two groups of atoms, there are no external forces, but internal forces between two groups. Berk. ___ 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 _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 41, Issue 73 * ___ 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] AFM Pulling and com motion
Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! ___ 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] stopcom and acc_grps
Hi all， When I use acc_grps (e.g.: SOL), I think I should not use com motion removal on that group, even the whole system. Am I right? Thanks ___ 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] freeze groups and com motion
Dear Fellow Users, I am modeling a system of a monolayer adsorbed on a water/solid interface. I just freeze the solid substrate, and I use ewald_geometry = 3dc in the mdp file (a vaccum boundary is upon the water). As the mass of the monolayer is 3 times less than the substrate, and 13 times less than the solvent, I am not sure whether or not I should remove the com motion of the whole system. Does anyone have any suggestions? Thank you ___ 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] Re: freeze groups and com motion (Berk Hess)
Thanks to David and Berk. Another question is, if the movement of the monolayer in the z direction is very small, drived by the Van de Waals interaction between the monolayer and substrate, could I just stopcm the monolayer+water regardless of the artifacts? Does the artifacts matter much in this case? I test two systems with stopcm and without stopcm, the monolayer does move down to be adsorbed on the substrate, but it drifts in xy plane in the system without stopcm. The data after its adsoption is needed. Thank you! Zhou Bo wrote: Dear Fellow Users, I am modeling a system of a monolayer adsorbed on a water/solid interface. I just freeze the solid substrate, and I use ewald_geometry = 3dc in the mdp file (a vaccum boundary is upon the water). As the mass of the monolayer is 3 times less than the substrate, and 13 times less than the solvent, I am not sure whether or not I should remove the com motion of the whole system. Does anyone have any suggestions? don't do anything else to stuff you've frozen (e.g. no constraints either). you can stopcm the monolayer+water, or separate. What you would want is stopcm only the xy components of monolayer+water. If you also stop z you get artifacts, as you have an absolute reference in z. I think that in the current version this is not possible. In Gromacs 4.0 this will be possible with uniform walls. But we probably should add a xy only mdp option for stopcom. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 41, Issue 17 * ___ 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] questions about simulation of water/solid interface
Hi all, I want to simulate a water/solid interface, like water on a HOPG surface. I have some questions in construction of the system: The system have a two-layer graphite surface (in the bottom of the box) , a 3 nm thickness of water layer on it, and a vacuum region on the water. Questions: 1) I have to freeze the two-layer graphite surface, NVT ensemble is better to use than NPT. Am I right? 2) Should I remove the com motion when I put a protein into the water, because of the frozen groups ? 3) I set the minimal distance between the graphite and the edge of box to 0.5 nm (half of the cutoff), but I found some water slipped out of the interface just from the box edge. Does anyone have suggestions to do such a system? I think if I set the distance less than 0.5nm, the water maybe not slip out. Although the interface will interact with itself for the unreasonable distance, it does not matter because it is just a frozen group. May it is a stupid idea. Thank you Bo Zhou ___ 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
