Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

Dear Bratin, When I am using a semiisotropic condition the pbc box is deforming/compressing pushing the lipid bilayer apart. I am attaching the screenshots of the system at the beginning(normal.png) of production run as well as at the end of 30ns simulation (elongated.png) for your reference.

[gmx-users] MD Simulation Time Is Slow

*Hi,* I am using gromacs and I would like to enhance my MD simulations time run on the servers. I execute the following command: gmx mdrun -nt 24 -s full.tpr -e full1.edr -o full1.trr -c p4iw_full1.gro -g flog1.log For 100 ps it took about 1 hr (as I can see from the log file) Time:

[gmx-users] GROMACS 2019.3 patch release available

Hi GROMACS users, The official release of GROMACS 2019.3 is available! This third patch release fixes several issues found since the second patch release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.3. Please see the link to the release notes below for more

Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

Hi Why you want to do isotropic? On Fri 14 Jun, 2019, 12:16 PM Prasanth G, Research Scholar, < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > > Can someone please tell me if it is okay to use isotropic pcoupltype for a > membrane protein simulation? Are there any disadvantages? > > Also,

[gmx-users] Membrane protein simulation isotropic vs semiisotropic

Dear all, Can someone please tell me if it is okay to use isotropic pcoupltype for a membrane protein simulation? Are there any disadvantages? Also, why is semiisotropic preferred over isotropic, in membrane protein simulations.. Thank you. -- Regards, Prasanth. -- Gromacs Users mailing list