[gmx-users] GROMACS 2018.x installation

Hi all: I am having trouble installing gromacs-2018.x (x = 1 to 3) on Ubuntu 18.04.  I invoked cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on on a simple i7-7700 machine with a GTX-970 GPU.  In both cases, everything went until make check, at which point a series

Re: [gmx-users] Groove width

Curves+ and 3DNA are standard tools for getting helical parameters.  You can find them pretty easily on Google. Gregory On 6/2/2018 5:06 AM, sp...@iacs.res.in wrote: Hi all I am doing simulation of DNA molecule. I want to calculate groove width of DNA in GROMACS. How to do this? Someone

Re: [gmx-users] Help with interpreting message for fatal error

18 at 4:49 PM, Gregory Poon <gp...@gsu.edu> wrote: Since there hasn't been any response to your question yet, may I ask: is it reproducible? Gregory On 3/11/2018 7:30 AM, Viveca Lindahl wrote: Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the

Re: [gmx-users] Help with interpreting message for fatal error

Since there hasn't been any response to your question yet, may I ask: is it reproducible? Gregory On 3/11/2018 7:30 AM, Viveca Lindahl wrote: Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of

Re: [gmx-users] Updating/upgrading GROMACS

/GMXRC This way you can easily switch between versions, compare, or keep working concurrently on different projects with the same version that you started out with! Cheers, -- Szilárd On Thu, Mar 2, 2017 at 6:02 PM, Gregory Poon <gp...@gsu.edu> wrote: Hello all: I would like to get some

[gmx-users] Updating/upgrading GROMACS

Hello all: I would like to get some advice on updating/upgrading an existing GROMACS installation. I realize that this may actually be a more general UNIX/ubuntu question, but I really would like to not foul this up on the local machines that we really need to keep running. In particular,

Re: [gmx-users] hbond

On 12/1/2016 7:45 AM, Justin Lemkul wrote: On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote: Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water

Re: [gmx-users] Regarding trjconv

On 11/17/2016 10:19 AM, Justin Lemkul wrote: On 11/17/16 10:13 AM, Apramita Chand wrote: Dear All, Thanks for your explanation, Erik. I just want to know whether applying trjconv will affect my calculations of other values like radial distribution functions ,hydrogen bond properties. Before

[gmx-users] gmx velacc

Hello to everyone: I am trying to use velacc to compute the diffusion constant of a globular protein that I have simulated for 100 ns. I am having a hard time figuring out how to have the index.ndx file "the index group consist of molecule numbers instead of atom numbers." What exactly are

[gmx-users] Position restraints for water during EM

Hello all: I would like to know where it is specified that waters are position-restrained during energy minimization. I can see that there is a #ifdef block for restraining the water, but I don't know where it is actually called. The .mdp files I use for EM (which I adapted from tutorials)

Re: [gmx-users] EM replicates

, but it has a default seed, resulting in deterministic random numbers :) Hope it helps, Tsjerk On Apr 9, 2016 00:33, "Gregory Poon" <gp...@gsu.edu> wrote: Hello all! I am wondering if the solvate, genion, and energy minimization (using steepest descent) procedures are determ

[gmx-users] EM replicates

Hello all! I am wondering if the solvate, genion, and energy minimization (using steepest descent) procedures are deterministic. I have been performing replicate energy minimization of a duplex DNA structure, always starting from scratch (i.e., pdb2gmx) and using the same parameters in terms

[gmx-users] Using CHARMM36 in GROMACS

Hello everyone, I am learning how to perform dynamics on double-stranded DNA sequences using the CHARMM36 FF I downloaded from the MacKerell lab. I have consulted the GROMACS documentation page regarding specific settings in the .mdp file for CHARMM36