Re: [gmx-users] Problem with removing COM translation
On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? cheers, m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with removing COM translation
Em 13-08-2010 14:24, ms escreveu: On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? The idea is to have less water molecules and, consequently, faster simulations. cheers, m. ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with removing COM translation
On 13/08/10 18:30, Alexandre Suman de Araujo wrote: I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? The idea is to have less water molecules and, consequently, faster simulations. I thought about that, but I guessed you can use a non-cubical box to do (roughly) the same. It seems a nice idea, at a glance. cheers, m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with removing COM translation
Hi Gmxers I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
