[gmx-users] CHARMM-GUI to GROMACS

2013-10-21 Thread Zhi Yue
Dear all, I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do equilibration by GROMACS. I know GROMACS can build the system, but my subsequent production run must be conducted by CHARMM. I want to use GROMACS to do equilibration cuz it may take long to get it equilibrated.

Re: [gmx-users] CHARMM-GUI to GROMACS

2013-10-21 Thread Justin Lemkul
On 10/21/13 11:14 AM, Zhi Yue wrote: Dear all, I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do equilibration by GROMACS. I know GROMACS can build the system, but my subsequent production run must be conducted by CHARMM. I want to use GROMACS to do equilibration cuz

Re: [gmx-users] CHARMM-GUI to GROMACS

2013-10-21 Thread Zhi Yue
Hi Justin, Thanks for your advice. I'll try again. Have a wonderful night! Best Shane On Mon, Oct 21, 2013 at 6:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/21/13 11:14 AM, Zhi Yue wrote: Dear all, I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do

[gmx-users] charmm-gui and gromacs

2012-02-12 Thread xiaojiong
Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] charmm-gui and gromacs

2012-02-12 Thread Mark Abraham
On 13/02/2012 12:15 PM, xiaojiong wrote: Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! You can probably write a .pdb coordinate file from any

[gmx-users] CHARMM GUI to Gromacs

2011-10-17 Thread Roy Lee
Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Before that, i had actually

Re: [gmx-users] CHARMM GUI to Gromacs

2011-10-17 Thread bipin singh
There is already tutorial for creating lipid bilayer and insertion of protein into that for GROMACS http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html Why you have used Charmmgui I am not able to understand. You can get some useful topologies from