[gmx-users] Converting top or tpr to psf

Hi, Does anyone have any experience with creating a psf file from a gromacs topology? I have a collaborator who uses NAMD and they are going to analyse some of my gromacs simulations together with some of their simulations but need psf files to do that. Many thanks and best wishes James --

[gmx-users] GROMACS 2018 official release

Hi GROMACS users, The official release of GROMACS 2018 is now available. What new things can you expect? Please see the release notes highlights at http://manual.gromacs.org/documentation/2018/release-notes/index.html. You can find the code, manual, release notes, installation instructions and

Re: [gmx-users] clayff

Hi, Those are the nonbonded parameters for kaolinite. Hope it gonna help you. ao13 26.9815386 1.5750 A 4.2712357244e-01 5.5638832000e-06 st14 28.085 2.1000 A 3.3020270089e-01 7.700652e-06 ob 8 15.9994000 -1.0500 A 3.1655413253e-01 6.501936e-01 oh

Re: [gmx-users] Heat capacity calculations from fluctuations and using g_dos

Den 2018-01-10 kl. 09:04, skrev Srinath Kompella: Hello all, I've simulated Methylcyclohexane (MCH) in NVT and NPT ensembles using GROMACS-5.1.4, from which I want to calculate the heat capacities (Cv and Cp respectively) of MCH. If I use the fluctuation properties, I get the

Re: [gmx-users] dimensions of the box

Dear Justin I would like to add here something that is happening in my gromacs simulation. I am trying to extend timulation to another 50ns. commands as follows gmx convert-tpr -s alz.tpr -extend 5 -o extend.tpr gmx mdrun -v -deffnm extend -gpu_id 00 -nt 4 it shows 15 days for the

Re: [gmx-users] What is the most reliable way to run repeats for reproducibility?

Hi Mark, Thank you very much. ) For the link you provide, I think I could not manipulate most of the computer resources, as I submit my jobs to our cluster, and the jobs are distributed to different available cores randomly. ) For "random seed" of velocity, I found here and I enabled this

Re: [gmx-users] What is the most reliable way to run repeats for reproducibility?

Hi, See http://www.gromacs.org/Documentation/Terminology/Reproducibility. Some people think they want reproducibility of a trajectory, which is generally not needed, and not consistent with highly efficient sampling (particularly with GPUs involved). But what you actually want is not

[gmx-users] Gnuplot x-axis range Represents Frames

Dear Gromacs Users I plotted my .gnu file in gnuplot. This plot x-axis range [0.000:7002.000], this data separated with xtic values as 0,1000,2000,...7000 (frame numbers) on x axis. While i want to change/multiply/transform this frame number into nano second, so that my x-axis values showed

[gmx-users] What is the most reliable way to run repeats for reproducibility?

Dear Gromacs, I can think of different ways of running repeats, after reading Justin's lysozyme tutorial. The 1st way: all starting from the same em.tpr after energy minimization (EM) and use em.tpr individually for subsequent steps (NVT, NPT and production MD): ) repeat 1: same em.tpr ?? NVT

Re: [gmx-users] Worse GROMACS performance with better specs?

Dear Jason, 1.) we have observed a similar behavior comparing Intel Silver 4114 against E5-2630v4 processors in a server with one GTX 1080Ti. Both CPUs have 10 cores and run at 2.2 GHz. Using our standard benchmark systems (see https://arxiv.org/abs/1507.00898) we were able to get 74.4 ns/day

[gmx-users] Heat capacity calculations from fluctuations and using g_dos

Hello all, I've simulated Methylcyclohexane (MCH) in NVT and NPT ensembles using GROMACS-5.1.4, from which I want to calculate the heat capacities (Cv and Cp respectively) of MCH. If I use the fluctuation properties, I get the following note: "Heat capacities obtained from