Re: [gmx-users] error on opening gmx_mpi

Shi, Thanks fo the note Yes, somehow - there is a version of gromacs 5 that is being summoned. I’ve got clean up my act a bit. A suggestion was made to try to use the mpi version because of the CPU I am using. gmx v18.3 was installed , but I removed its build and built the 19.1 beta m

Re: [gmx-users] error on opening gmx_mpi

> > Message: 3 > Date: Tue, 18 Dec 2018 15:12:00 -0600 > From: p buscemi > To: "=?utf-8?Q?gmx-users=40gromacs.org?=" > Subject: [gmx-users] error on opening gmx_mpi > Message-ID: > <1545164001.local-b6243977-9380-v1.5.3-420ce...@getmailspring.com> > Content-Type: text/plain; charset="utf-8

Re: [gmx-users] error on opening gmx_mpi

Justin, thank you very much for the rapid response. I read that the same way, but I’m a bit confused. Is "mdrun_mpi version 5.1.2 in /usr/bin” a result of an install of v5 of gromacs ( have not used that version ) or a result of an install of a v5 of mpi ? i.e. not sure where that came

[gmx-users] Impromised X-mas developer conference 1h earlier tomorrow?

Hi! Merry Christmas/Happy Hanukkah/Great Gromacs-Release-Day or whatever you might be celebrating the next two weeks :-) Mark Abraham is on his annual very well-deserved vacation in Australia, and tomorrow we have a christmas party at SciLifeLab in Stockholm starting at 5pm. However, it would st

Re: [gmx-users] Calculating Contact Surface Area in one Graph

On Tue, Dec 18, 2018 at 2:34 PM Sebastian Muraru < sebastian.mur...@grabtop.upb.ro> wrote: > Hi there! > > I am a Masters student trying to figure things out. I am trying to > calculate the contact surface area between two molecules. I am aware of the > classic formula, which is CSA = (SASA(comple

Re: [gmx-users] error on opening gmx_mpi

On Tue, Dec 18, 2018 at 4:12 PM p buscemi wrote: > I installed 2019 beata gmx_mpi with: > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on > -DCMAKE_CXX_COMPILER=/usr/bin/g++-7 -DCMAKE_C_COMPILER=/usr/bin/gcc-7 > -DGMX_MPI=ON -DGMX_USE_OPENCL=ON > > The install completed

[gmx-users] error on opening gmx_mpi

I installed 2019 beata gmx_mpi with: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_CXX_COMPILER=/usr/bin/g++-7 -DCMAKE_C_COMPILER=/usr/bin/gcc-7 -DGMX_MPI=ON -DGMX_USE_OPENCL=ON The install completed with no errors. I need to take this step by step: in runnin

[gmx-users] Calculating Contact Surface Area in one Graph

Hi there! I am a Masters student trying to figure things out. I am trying to calculate the contact surface area between two molecules. I am aware of the classic formula, which is CSA = (SASA(complex) - (SASA(molecule1) + SASA(molecule2) ) ) divided by 2 and I am aware that we can make graphs fo

[gmx-users] Simulation Across Mulitple Nodes with GPUs and PME

Hello, I have a quick question about how GROMACs 2018.5 distributes GPU resources across multiple nodes all running one simulation. Reading the documentation, I think it says that only 1 GPU can be assigned to the PME calculation. Is it then true if I had 10 nodes each with 4 GPUs all working on

Re: [gmx-users] Install GROMACS 2018 with CUDA features in dynamic linking way

Your suspicion might be valid, but it I'd prefer if you could verify this through more standard means too; if you confirm that requesting dynamic cudart linking is not honored, than there might be an issue in the GROMACS build system. BTW, on my binary I built with -DCUDA_USE_STATIC_CUDA_RUNTIME=O

Re: [gmx-users] contact analysis between the all backbone of same protein

Hi, You can obtain the backbone atom contacts in the same protein using the gmx mdmat command. gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5 (the -t option is because you want the protein contacts within 0.5 nm I guess). When prompted, select the correct group from index file.

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Tue, Dec 18, 2018 at 12:17 AM Sri Prasanth Ghanta, Doctoral Research Scholar, Biosciences, SSSIHL wrote: > Dear all, > > I have started following the new tutorial > and the old tutorial > < > http://www.bevanlab.biochem.vt.edu/Pages/Personal/

Re: [gmx-users] Running simulation differences

On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi again Justin, > > I've been thinking about the normal variability between MD simulations you > commented. I am simulating the interaction of a lipid with water, but the > van der waals energ

Re: [gmx-users] Running simulation differences

Hi again Justin, I've been thinking about the normal variability between MD simulations you commented. I am simulating the interaction of a lipid with water, but the van der waals energy value that I obtain (-257.25 ± 35.86 kj/mol) for me is considerably different from the published value (-36

Re: [gmx-users] bonded interaction larger than cutoff

Thanks Dr. Lumkel On Mon, Dec 17, 2018 at 2:30 PM Justin Lemkul wrote: > On Mon, Dec 17, 2018 at 7:48 AM Quyen Vu Van wrote: > > > Dear all, > > I add a harmonic bond between two ends of my molecule (then my molecule > > will have circle shape) with hope to calculate the force opens my > molecu