[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Dear Justin, Thanks for your answers and helps. My mdrun was finished. > If you want specific help about why you're observing some given > speed/performance, you need to provide actual details about the simulated > system, hardware, etc. and upload full .log files to a file-sharing service >

Re: [gmx-users] Umbrella sampling

On 9/5/16 3:16 AM, masoud aliyar wrote: Hi everybody I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything is ok but some aspects of the procedure remain a bit unclear to me. Why don’t we need to do NVT equilibration before first MD? And why pull codes Equilibrate however

[gmx-users] Membrane Simulation in Gromacs - Extracting waters from hydrophobic region

Hi Gromacs users. Our lab is working on membrane simulations using gromacs. The main problem to build a system is extract waters from aliphatic carbons. Gromacs website have a script called keepbyz.sh (link: (link: http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations) but it have

[gmx-users] optimizing cluster and simulation setup: Webinar

Hi, The teams in Göttingen and Stockholm did a thorough study on optimizing the setup of GROMACS on various hardware systems. Due to the big interest in the topic we are organizing a free webinar this Wednesday, 7th Sept., from 16:00 CEST. Presenter will be Carsten Kutzner. At the end of

[gmx-users] Umbrella sampling

Hi everybody I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything is ok but some aspects of the procedure remain a bit unclear to me. Why don’t we need to do NVT equilibration before first MD? And why pull codes are applied during NPT equilibration of selected windows or