[gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?
Dear all: I am working on a research to study whether the Lateral pressure profile influence the protein function. To get different lateral pressure profile, I used Parinello-Rahman P coupling method and anisotropic pressure coupling with different p_ref values(such as 0.9bar, 1bar, 1.1bar, .,2bar) in xy. I wonder whether this method feasible. If it is not feasible, could anyone please give me a hint on how to do it. Thank you KONG Xian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?
Dear Justin A. Lemkul: Thanks for your rapid reply. Just as you said, the result of my simulation with different xy p_ref values didn't vary, they are almost the same. I think I need consider some other ways to do what I was mean to do. I have read a paper that study the different lateral pressure profiles of lipid membrane with respect to sterol type, I think I may chose this as a way to produce different pressure profiles. Ollila, O. H. S., T. Rog, et al. (2007). "Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol." Journal of Structural Biology 159(2): 311-323. And, what's more, Do you think steered MD is a choice? KONG Xian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] re: How to exert different lateral pressure profile of a lipid membrane
KONG Xian wrote: > Dear Justin A. Lemkul: > > Thanks for your rapid reply. > > Just as you said, the result of my simulation with different > xy p_ref values didn t vary, they are almost the same. > > I think I need consider some other ways to do what I was mean > to do. > > > > I have read a paper that study the different lateral pressure profiles > of lipid membrane with respect to sterol type, I think I may chose > this as a way to produce different pressure profiles. > > >Membranes themselves are far more responsive to changes in pressure than are proteins, so unless there is a >considerable difference in the lipid properties and also considerable interplay between the lipid dynamics >and those of the protein, you still won't see any difference. Again, I'd be skeptical that you'd ever find >anything meaningful by changing the pressure in increments of 0.1 bar. I just find a relevant paper. They control the target pressure in the xy plane to 10 bar while keep the z target pressure 1 bar, thus producing a surface tension. They intend to study the mechanosensitivity of a protein. I think it's a nice implication for me. FISCHER, G., KOSINSKA-ERIKSSON, U., APONTE-SANTAMARIA, C., PALMGREN, M., GEIJER, C., HEDFALK, K., HOHMANN, S., DE GROOT, B. L., NEUTZE, R. & LINDKVIST-PETERSSON, K. 2009. Crystal Structure of a Yeast Aquaporin at 1.15 angstrom Reveals a Novel Gating Mechanism. Plos Biology, 7 > > /Ollila, O. H. S., T. Rog, et al. (2007). "Role of sterol type on > lateral pressure profiles of lipid membranes affecting membrane > protein > functionality: Comparison between cholesterol, desmosterol, > 7-dehydrocholesterol and ketosterol." _Journal of Structural Biology_ > *159*(2): 311-323./ > > > > And, what s more, Do you think steered MD is a choice? > > > What would you steer? Doesn't sound applicable here. I haven't think too much on this method. I thought I could exert some force on the atoms that are close with lipids, namely those atoms that are on the surface of the protein， thus mimicking the effects of the membrane lipids on the protein. It's not a mature thoughts, I think I should think it for a little longer time. Thanks for your kindly discussion which is inspirational. KONG Xian THU, Beijing __ Information from ESET NOD32 Antivirus, version of virus signature database 6328 (20110727) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
I have sent this email days ago, but I got no answer. Hope someone would saw it this time. Sorry for disturbing. Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] 答复: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
Thanks for your important advice, I am extending my simulation to 60ns, if it is still not long enough, I’ll extend another time. Thank you. 发件人: Jianguo Li [mailto:ljg...@yahoo.com.sg] 发送时间: 2011年8月22日 9:52 收件人: KONG Xian 主题: Re: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure Thanks for your kindly reply. I used the LINCS calculated the pressure field. The distinct between protein and the lipid bilayer is obvious from the pressure field. But the lipid bilayer and the water is not very obvious , they seems to be a uniform from the pressure field calculated. As in Ollila’s original paper: 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes, there is an distinct separation region between membrane and the water. Maybe the LINCS is the problem. Another problem is perhaps the localpressure software is for CG model? My model is all-atom model and the simulation time length is not long enough, maybe this is the cause of the results? >From my limited experience, the local pressure calculation converges very >poorly. It takes more than 50 ns of production run in my case to get a >converged profile. You can divide the production run into several >sub-trajectories to judge the convergence. KONG Xian 2011/8/21 Hi, Kong Xian, It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 9, 3882b3893. best regards, Jianguo From: KONG Xian To: gmx-users@gromacs.org Sent: Friday, 19 August 2011 23:50:01 Subject: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure I have sent this email days ago, but I got no answer. Hope someone would saw it this time. Sorry for disturbing. Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China __ Information from ESET NOD32 Antivirus, version of virus signature database 6397 (20110821) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __ Information from ESET NOD32 Antivirus, version of virus signature database 6398 (20110821) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to handle different atom names between pdb and rtp files.
Hello, I've got a pdb file,but while I convert it to gro files, I met such problem: Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms I find that in the rtp files of the ff files, the H atom linked with C-alpha is called H, but in the pdb file, the same hydrogen atom is called HA, I think this may be the problem. So, my problem is, how to convert my pdb files to make the atom names consistent between the pdb and rtp files? KONG Xian Tsinghua University, Beijing, China 2011/9/13 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
