Re: [gmx-users] Normal-mode analysis in Gromacs

Den 2018-03-08 kl. 00:53, skrev Kevin C Chan: Dear Users, I have encountered several questions when I try to perform NMA on a protein structure from an equilibrated MD simulation. I were basically referred to the gromacs manual (

[gmx-users] Hamiltonian replica exchange in gromacs 4.6.7

Hello everybody, So i am trying to set up a replica exchange with solute tempering simulation for my membrane-drug systems. We modified the gromacs source code in a way that allows the modification of the hamiltonian of singular pairs of interactions (eg solute-water, solute-solute, ion-solute

[gmx-users] OPLS-AA parameters for dimethylsiloxane

Hi all, Before I start possibly reinventing the wheel, does anyone here have a decent OPLS-AA topology for dimethylsiloxane? LipParGen produces a topology, but for a different FF, and the otherwise excellent OPLS-AA topology builder from ERG fails outright. Not exactly a Gromacs question, I know.

[gmx-users] viscosity calculation using Green-Kubo

Hello, I would like to calculate viscosity using the Green-Kubo method. I understand that the viscosity calculation using g_energy uses the msd method. Is there any built in command in gromacs for green-kubo? Or would I need to do that by hand? Thanks, Jo -- Gromacs Users mailing list *

[gmx-users] viscosity calculation using g_energy

Hello, I would like to calculate viscosity of a box of water using g_energy. I used the line g_energy -f production.edr -vis viscosity.xvg, where the viscosity.xvg generated shows bulk and shear viscosity (cP) by time (ps). However, the value are several orders of magnitude above the correct

[gmx-users] X2top error, Could only find a forcefield type for 0 out of 66 atoms

Dear Gromacs users, I am trying to transform my PDP file for AL2O3 surface to a top file using x2top. I have defined my forcefield.itp and .n2t file. However, I keep recieving an error telling me that "Could only find a forcefield type for 0 out of 66 atoms" my PDB file looks like COMPND

Re: [gmx-users] thermostat and barostat

Hi, The pressure coupling algorithms operate globally (but possibly anisotropically) Mark On Wed, Mar 7, 2018, 17:43 Faezeh Pousaneh wrote: > Hi, > > I simulate a system which is very sensitive to chosen thermostat and > barostat. I see information in > Gromacs webpage (*

[gmx-users] thermostat and barostat

Hi, I simulate a system which is very sensitive to chosen thermostat and barostat. I see information in Gromacs webpage (*http://www.gromacs.org/Documentation/Terminology/Thermostats *) that some thermostat are not good for systems

Re: [gmx-users] Fw: Geometry Optimization for Metal organic Frame works

Hi, i am also simulating MOFs with gromacs and can say that OBGMX is not the best way to generate the topology file. It has many flaws but shows some ideas. I am currently creating my own forcefield using the UFF4MOF by M. Addicoat. You can have a look at it:

Re: [gmx-users] Gromacs Tutorial by Justin

Thank you. Best regards On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul wrote: > > > On 3/7/18 6:24 AM, Faezeh Pousaneh wrote: > >> Dear Justin, >> >> I have 2 questions regarding your tutorial on Carbon Dioxide in this link: >>

Re: [gmx-users] Geometry Optimization for Metal organic Frame works

I would contact the OBGMX folks concerning this, as it sound like a software issue. If it works to produce a topology file for your initial coordinate system but not your optimized coordinates (presuming the same system composition, just modified geometry) than something seems amiss with their

[gmx-users] Fw: Geometry Optimization for Metal organic Frame works

Thank You Micholas I have created the topology files using initial input file in OBGMX and it shows that there are 20 unique bond terms, out of which there are 3 bonds between the metal ion and the N2 in linker. However, when I tried to create topolgies using the optimized final output

Re: [gmx-users] segmentation fault

On 3/7/18 6:11 AM, sp...@iacs.res.in wrote: Hii all I am trying to simulate biomolecule in Guanidinium chloride in AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in energy minimization step but in NVT

Re: [gmx-users] Gromacs Tutorial by Justin

On 3/7/18 6:24 AM, Faezeh Pousaneh wrote: Dear Justin, I have 2 questions regarding your tutorial on Carbon Dioxide in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html 1- I see that in your simple simulation you use no boundary conditions,

[gmx-users] Gromacs Tutorial by Justin

Dear Justin, I have 2 questions regarding your tutorial on Carbon Dioxide in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html 1- I see that in your simple simulation you use no boundary conditions, pbc=no, should it be always so for this model?