Re: [gmx-users] How to install gromacs on cpu cluster

Hi Yeping, A full build may be helpful to run the initial correctness tests, once you have done this can then use -DGMX_BUILD_MDRUN_ONLY=on for production runs. Having a full version of GROMACS on a node with access to the same file system where you do runs is also helpful since there may be

Re: [gmx-users] missing prepare-qmmm.py

Hello, After compiling GROMACS with the MiMiC option, I was not able to locate the prepare-qmmm.py file. I do not know whether this is a result of a faulty installation or if it is something else I used the following flags: -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_DOUBLE=ON

[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

Dear all, I have been trying to use gmx gangle for the calculation of the following angle : I have a group of 3 residues and another group of 4 residues. I want to define a vector which goes through the center of mass of these two groups and I am interested in calculating the angle of the vector

Re: [gmx-users] How to install gromacs on cpu cluster

Hi Benson, I feel I may need to add the following options to cmake? -DGMX_MPI=on -DGMX_SIMD=xxx -DGMX_BUILD_MDRUN_ONLY=on Should I? -- From:孙业平 Sent At:2019 Jun. 30 (Sun.) 08:36 To:gromacs ; Benson Muite Subject:Re: [gmx-users]

[gmx-users] Error on scaling the charges

Dear Gromacs Users, I'm simulating an ionic liquid with AMBER 99sb-ildn ff in GROMACS 5.1.4 package. With charges +1 and -1 on the cation and anion respectively, the system is neutral and the minimization is okay. But on scaling the charges by 0.8, the total charge shows to be above 6000, for a

Re: [gmx-users] missing prepare-qmmm.py

Hi, Was -DCMAKE_PREFIX_PATH set to the location at which CommLib library was installed? Not sure if -DCMAKE_INSTALL_PREFIX:PATH=/home/derk/Prog/gmx19 is a typo and should be -DCMAKE_INSTALL_PREFIX_PATH=/home/derk/Prog/gmx19 prepare-qmmm.py does not seem to be in the sources at

[gmx-users] a99SB-disp forcefield

Dear Gromacs users, I am looking to use the a99SB-disp forcefield from Robustelli et al. PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3. The details of the forcefield are in the paper supplementary material. I have carried out the following steps: - Downloaded the

Re: [gmx-users] Error in creating parameter files using SwissParam

This is nothing to do with the GROMACS software, you should be asking http://www.swissparam.ch/ The error seems to be self explanatory, did you check your mol2 file? http://www.swissparam.ch/SwissParam_mol2_file.html I would suggest loading the mol2 file you have using pymol or vmd, and check to

[gmx-users] Error in creating parameter files using SwissParam

Dear GROMACS users and developers, I want to run MD simulation of a protein bound to FAD using CHARMM36 force field. However, I need to generate the parameter files of FAD first. Hence, I followed the following steps: 1. Downloaded the .pdb structure file from RCSB PDB databank 2. Kept