[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?

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

[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?

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-us

[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 wa

[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

? 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&#

[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

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] 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

[gmx-users] how to handle different atom names between pdb and rtp files.

, 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@gromac