[gmx-users] Tilt angle distribution

Dear users, I am working on ctab/water surfactant system and got stuck with the calculation of tilt angle distribution of hydrocarbon chain. Is there any tool to calculate the tilt angle distribution in gromacs. Please specify the way to do that... -- Gromacs Users mailing list * Please search t

[gmx-users] question about polar.mdp file in MMPBSA

Dear all I RUN MOLECULAR SIMULATION FOR DNA-SMALL MOLECULE COMPLEX (50 NS), I WANT TO ANALYSIS USING MMPBSA, FOR POLAR SOLVATION ENERGY CALCULATION , I USED THE MMPBSA.MDP [1] OBTAINED FROM HTTPS://RASHMIKUMARI.GITHUB.IO/G_MMPBSA/HOW-TO-RUN.HTML. I THINK THERE IS SOME PROBLEM, BECAUSE AFT

[gmx-users] umberlla sampling of protein ligand complex

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said: Acetyl

[gmx-users] coulombic terms clarification

Hi all, A quick question -- I just wanted to double check that the Coulomb-SR term does NOT include the Coulomb-14 term.(To me, the "SR" label is somewhat misleading as it makes me think that it includes "everything" short ranged). In other words, if one wishes to know the total Coulombic en

Re: [gmx-users] coulombic terms clarification

On 5/28/19 7:49 AM, Mala L Radhakrishnan wrote: Hi all, A quick question -- I just wanted to double check that the Coulomb-SR term does NOT include the Coulomb-14 term.(To me, the "SR" label is somewhat misleading as it makes me think that it includes "everything" short ranged). In othe

Re: [gmx-users] coulombic terms clarification

thank you! Mala On Tue, May 28, 2019 at 8:01 AM Justin Lemkul wrote: > > > On 5/28/19 7:49 AM, Mala L Radhakrishnan wrote: > > Hi all, > > > > A quick question -- I just wanted to double check that the Coulomb-SR > term > > does NOT include the Coulomb-14 term.(To me, the "SR" label is > s

Re: [gmx-users] gmx trjconv

Dear all, Any comment on this, please? Thank you. Alexander On Thu, May 23, 2019 at 10:02 AM Alex wrote: > Dear GMX user, > I have a 110 GB trajectory from which I would like to extract only the > trajectory of the part of my interest, the rest is water. To do so, I use " > echo 1 | mpiexec_mpt

Re: [gmx-users] gmx trjconv

Hi, You can use trjcat On Tue 28 May, 2019, 6:10 PM Alex, wrote: > Dear all, > Any comment on this, please? > > Thank you. > Alexander > > On Thu, May 23, 2019 at 10:02 AM Alex wrote: > > > Dear GMX user, > > I have a 110 GB trajectory from which I would like to extract only the > > traject

[gmx-users] Stress-Strain curve plot

Hi all, I’m running GROMACS to simulate a simple phospholipid bilayer membrane (POPC) under deformation, and plot the von Mises stress-strain curve to determine yielding point. I have got the membrane deformed and extractred output pressures from .edr file (option PRESS X, PRESS Y, PRESS Z) to

[gmx-users] Parrinello-Rahman vs. Nose-Hoover

Hi all, In GROMACS Manual, it is said that "In most cases Parrinello-Rahman barostat would be combined with the Nose-Hoover thermostat as the most practical choice", and I see that Nose-Hoover algorithm is only available for temperature coupling, not pressure coupling. Why is Nose-Hoover not used

Re: [gmx-users] Parrinello-Rahman vs. Nose-Hoover

Hi, Why should it be used? :-) Mark On Tue, 28 May 2019 at 23:28, Anh Vo wrote: > Hi all, > > In GROMACS Manual, it is said that "In most cases Parrinello-Rahman > barostat would be combined with the Nose-Hoover thermostat as the most > practical choice", and I see that Nose-Hoover algorithm i

Re: [gmx-users] Stress-Strain curve plot

Hi, On Tue, 28 May 2019 at 23:26, Anh Vo wrote: > Hi all, > > > I’m running GROMACS to simulate a simple phospholipid bilayer membrane > (POPC) under deformation, and plot the von Mises stress-strain curve to > determine yielding point. > > > > I have got the membrane deformed and extractred out

[gmx-users] FEP in vacuum simulation - inconsistent results among FEP methods

I am calculating the free energy change in transforming one small molecule into another by the simple removal of a CO2 from the first molecule, and also mutating some bond parameters slighty since the second molecule has a couple different atom types in GAFF without the CO2 attached to it. I analy

Re: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users, Is there a reason why segmentation fault appeared when gmx hbond command was used? Thank you, Neena From: Neena Susan Eappen Sent: Friday, May 24, 2019 12:40 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Segmentation

[gmx-users] Timestep in GROMACS simulation

Hi all, How did you choose your timestep and simulation time when running GROMACS? Is there any logic for deciding that? I’ve read that larger time step permits better sampling without significant errors in observed thermodynamic, structural or dynamic properties => What does “sampling” mean? Why

Re: [gmx-users] Timestep in GROMACS simulation

Hi, That totally depends on your forcefield. Most classical all-atom forcefields are recommended to be run with a 2 femtosecond timestep. Some coarse-grained forcefields like Martini can do 20+ fs, but you’ll want to check the literature. As for better sampling, you simply sample longer times for

[gmx-users] Explaination of some terminology

Hi all, I'm new to GROMACS and there are some terms that I’m not very clear when reading GROMACS materials. I have looked them up and read more but I’m still confused. Please help me to clarify them. - What is improper vs. proper dihedral? - It is said that “If a dynamical system i

Re: [gmx-users] Explaination of some terminology

Proper dihedrals deal with rotation around a bond i.e. for a chain C-C-C-C, the proper dihedral will encodes the potential energy versus angle curve for the rotation around the central -C-C- bond. From the GROMACS Manual http://manual.gromacs.org/current/reference-manual/functions/bonded-interacti

Re: [gmx-users] Segmentation fault, core dumped error

Would be a good idea to provide the exact command line used, and a copy of the exact output from the command. Copy and paste the text, don't type it out from memory. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University

Re: [gmx-users] Timestep in GROMACS simulation

Hi, I'm still not clear what "sampling" means. Does it mean collecting data from the simulation? Thank you very much for your answer. Best, Anh Vo -Original Message- > > > Message: 4 > > Date: Tue, 28 May 2019 20:43:32 -0400 > > From: Kevin Boyd > > > > Hi, > > > > That totally depe

Re: [gmx-users] Stress-Strain curve plot

Hi, 2. As I know, lower yield stress means the molecules are not holding together in the structure as well, and higher yield means that some change is happening later in GROMACS simulations. Together, they suggest that your chains are not pulling away from one another as quickly. In other words, t

Re: [gmx-users] Parrinello-Rahman vs. Nose-Hoover

Hi, Previously, as my colleague performed the same simulation with me (POPC bilayer membrane under equibiaxial tension) in LAMMPS, he could use Nose-Hoover for both temperature and pressure coupling. But in GROMACS when I tried to re-do what he has done, I could not use Nose-Hoover for pressure co

Re: [gmx-users] Parrinello-Rahman vs. Nose-Hoover

Different simulators use different thermostats and barostats, and given that molecular simulations are a lot like grandma's cooking, there is no truly clear answer to your question. However, I do have a few suggestions. If you want to recreate exactly what your colleague did, use LAMMPS -- its