Re: [gmx-users] autocorrelation function and residence time

Thank You On Fri, Sep 22, 2017 at 1:35 PM, Erik Marklund wrote: > Dear Tsaneem, > > Negative values don’t signify lack of correlation, but anticorrelation. > Also, by omitting negative values you introduce a slight bias in your fit > towards longer half-life. > > Kind regards, > Erik > _

[gmx-users] How to correctly setup gmx_mpi mdrun

Hi Gromacs Users, I'm learning how to run a simple replica exchange MD simulation on my own computer. My computer has 12 Xeon E5-2630 CPUs and 1 GeForce GTX 770 GPU. I used to compile gromacs without the -DGMX_MPI option and it runs fine for normal MD. I can control the number of CPUs to use by s

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

On 22/09/17 16:59, Sim gmx wrote: First of all, thanks for your replies! 1) Indeed, both epsilon-r and epsilon-rf are such constants. However, in the paper I guess that they refer to the relative dielectric constant of the reaction field, i.e. epsilon-rf. Or do I miss something ? Yes, they ar

[gmx-users] p-coupling for inverted hexagonal phase

Dear Gromacs users, I am doing a simulation on inverted hexagonal (HII) phase composed of just lipids and water. (please have a look at HII phase here: https://openi.nlm.nih.gov/detailedresult.php?img=PMC2695813_1757-5036-2-3-3&req=4 ) My question is regarding the pressure coupling for such syst

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

First of all, thanks for your replies! 1) Indeed, both epsilon-r and epsilon-rf are such constants. However, in the paper I guess that they refer to the relative dielectric constant of the reaction field, i.e. epsilon-rf. Or do I miss something ? 2) I will for sure contact them to collect all the

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

Hi, In addition to Mark's comments, there are a few other points to be aware of: 1. If you use the twin-range scheme (i.e. 0.8/1.4) with nstlist 5, you need to set nstcalclr to 1 to get results matching those as reported by Poger and co-workers (see http://pubs.acs.org/doi/abs/10.1021/acs.jctc

[gmx-users] restrained md_coordinate issue

Hello Everyone I have simulated a protein - ligand complex with gromacs 5.1.4 for 100ns. I have restrained the position of the ligand ( which in my case is hydrogen peroxide). Applied following commands for correcting pbc: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc -nojump -o file1.xtc gmx_mpi t

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

Hi, On Fri, Sep 22, 2017 at 10:21 AM Sim gmx wrote: > Hi! > > I would like to do simulations of lipids bilayers with gromos54a7 > parameters. To do so, I want to use the same mdp parameters as Poger et al. > (the authors). > > In their papers, they write : "Nonbonded interactions were evaluated

[gmx-users] Where can I find Gromos87 forcefield

Hi all,Where can I get gromos87 parameter file, with all atom types and atom definitions (.atp) file, similar to the one gromacs provides in gromacs/share/top/forcefiled.ffI understand the advantages and disadvantages of using gromos87, still I want to use the for

[gmx-users] Gromos54a7 electrostatics interactions ?

Hi! I would like to do simulations of lipids bilayers with gromos54a7 parameters. To do so, I want to use the same mdp parameters as Poger et al. (the authors). In their papers, they write : "Nonbonded interactions were evaluated using a twin-range cutoff scheme: interactions falling within the 0

Re: [gmx-users] autocorrelation function and residence time

Dear Tsaneem, Negative values don’t signify lack of correlation, but anticorrelation. Also, by omitting negative values you introduce a slight bias in your fit towards longer half-life. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie