Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

I have tried this command line: sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"

Re: [gmx-users] �ظ�: �ظ�: Re: Implicit Solvent and Box Size

Hi, As Justin mentioned, with implicit solvent, there is no "box". The solute is simply diffusing through space. The idea of a simulation box is only relevant when you are using PBC. Despite having box vectors present at the bottom of your .gro file, these don't really have a meaning if you're

[gmx-users] 回复: 回复: Re: Implicit Solvent and Box Size

Dear Justin, I made the box with 'gmx ediconf'. Should I add some constraints for the box boundary for non-pbc box? Would you please give more hints? Thank you very much! Regards, Zhuo 发件人: 张 卓 发送时间: 2019年10月8日 10:40 收件人:

[gmx-users] INFLATEGRO SHRINKING SCRIPT ERROR

hello everyone, I have been struggling with the automated script for shrinking iteration in Professor lemkul tutorials. can anyone spot what am I doing wrong here? * sh

Re: [gmx-users] [Performance] poor performance with NV V100

Hi, Can you please share your log files? we may be able to help with spotting performance issues or bottlenecks. However, note that for NVIDIA are the best source to aid you with reproducing their benchmark numbers, we Scaling across multiple GPUs requires some tuning of command line options,

Re: [gmx-users] ERROR :: Atomtype LC3 not found : KALP-15 in water tutorial

On 10/8/19 8:44 AM, Seketoulie Keretsu wrote: Dear Expert, While doing the KALP15 in DPPC tutorial, I came across this error. I have tried google search for solutions but couldn't resolve it. Would appreciate if you would kindly let me know how to move forward: INPUT COMMAND: gmx grompp -f

[gmx-users] ERROR :: Atomtype LC3 not found : KALP-15 in water tutorial

Dear Expert, While doing the KALP15 in DPPC tutorial, I came across this error. I have tried google search for solutions but couldn't resolve it. Would appreciate if you would kindly let me know how to move forward: INPUT COMMAND: gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p

Re: [gmx-users] 回复: Re: Implicit Solvent and Box Size

On 10/7/19 10:40 PM, 张 卓 wrote: Dear Justin, I have tried implicit solvent without pbc or barostat. The box was not compressed but the molecules flew out of the box. I believe that it was because of nopbc box. Would you please give more information on why implicit solvent is used without

Re: [gmx-users] Protein ligand simulation topology

On 10/8/19 7:30 AM, DEEPANSHU SINGLA wrote: Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as

[gmx-users] Protein ligand simulation topology

Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as follows: [molecules] ; Compound#mols

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

Hej, I can't access the repository, so I can't say for certain what happened. Can you share your cmake command line? Cheers Paul On 07/10/2019 21:25, Lyudmyla Dorosh wrote: Hello Gromacs Developers/Users, I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel compilers