Re: [gmx-users] To calculate temperture in a specific region

Hi, If you're after such a group-wise temperature at a single point in time, then you can e.g. use gmx select to make your selection, and then gmx traj to get the velocities for those atoms (if you recorded them from mdrun with nstvout). Mark On Tue, Sep 22, 2015 at 8:03 AM Krishna Mohan Gupta

[gmx-users] Crystallographic Ions

Hi Everyone, I'm working with a protein which contains 2 crystallographic sodium ions and am experiencing trouble making the .gro file using pdb2gro using the Charmm36.ff parameters. The two ions can be seen here: ATOM 29009 NANA 1 -18.056 -14.113 -24.865 1.00 0.00

[gmx-users] PMF calculation_ Constraint

Dear Gromacs users I want to calculate the PMF of tocopherol in DMPC bilayer system. For this means, I used Constraint method. the pull code in my .mdp file is : pull = constraint pull-geometry = distance;distance, direction, or cylinder pull-dim = N N Y pull-constr-tol = 1e-6 pull-start =

Re: [gmx-users] Prospective research areas of GROMACS

Hi, On Mon, Sep 21, 2015 at 7:10 PM Sabyasachi Sahoo wrote: > Dear Gromacs users and developers, > > I am a parallel programming researcher and would like to contribute to > Gromacs molecular dynamics software by helping to nail down any bottlenecks > that occur in

Re: [gmx-users] distance dependent energy

Hi, On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen wrote: > Dear Gromacs users, > > I would like to work out the energy (total and kinetic) as a function of > the distance from the center of mass of a droplet. However, using g_energy > just gave me the values as a function of

Re: [gmx-users] What's the practical effect of 'continuation = yes/no'?

Hi, On Tue, Sep 22, 2015 at 8:22 AM Trayder Thomas wrote: > What exactly does 'continuation = yes' do? > Tells mdrun to behave as though the simulation didn't stop :-) We need a way to let people stop the simulation, perhaps change something, and continue on with the

[gmx-users] To calculate temperture in a specific region

Dear Gromacs users, I need to calculate temperature of molecules in a particular region after equilibration run (NVT or NPT) but during simulation molecules will exchange from one region to another. Can anyone have any suggestion in this regards ? Thanks. Krishna

Re: [gmx-users] addition of hydronium ion in simulation box

Hi, > Hello justin, > > Thanks, actually I want to study movement of protons along the lenght of a > water channel. > > What you need is constant-pH MD, which is not natively supported in GROMACS. What Justin says. There is only a 3.3 version that currently supports this, which is available

[gmx-users] What's the practical effect of 'continuation = yes/no'?

What exactly does 'continuation = yes' do? My understanding thus far is that it will move particles in the first step (using the input velocities) before applying the constraints (LINCS bond lengths etc.). When continuing a simulation with 'continuation=no' you would apply constraints twice in a

Re: [gmx-users] distance dependent energy

Dear Van, Plot against the COM distance, which you can get as a function of time too. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road

Re: [gmx-users] To calculate temperture in a specific region

Thanks Mark, Actually, at a particular time I am able to calculate temperature in a region. But on taking average of few picosecond trajectory to minimize the statistical error, molecules exchange their location with surrounding region. Therefore, it is difficult to take average. Is there any

[gmx-users] Fwd: Diffusion of protein

Hello all I am trying to performed molecular dynamics simulation of ligand-protein complex in popc lipid with charmm36 force field. I am taking help from Justin A. Lemkul tutorial. I wanted to calculate the diffusion of the protein. Before performing the study I removed the PBC of my system. I

Re: [gmx-users] force fields selection

On 9/21/15 10:22 PM, James Lord wrote: Dear gmx users, I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein partitioning at biphasic liquid-liquid interfaces (Similar Justin's tutorial for biphasic system). Which one is recommended if anyone has experience with such system

Re: [gmx-users] SDF problem

On 9/22/15 8:14 AM, Daniele Veclani wrote: Dear gromacs user My system consist of 1 molecule + 1000 of solvents (water) in cubic box. I did 5 ns NPT equilibration and currently I am doing analysis stuff such as RDF, density, viscosity, etc. And now I want to try using g_spatial but I stuck

Re: [gmx-users] PMF calculation_ Constraint

On 9/22/15 3:46 PM, Sepideh Kavousi wrote: Dear Gromacs users I want to calculate the PMF of tocopherol in DMPC bilayer system. For this means, I used Constraint method. the pull code in my .mdp file is : pull = constraint pull-geometry = distance;distance, direction, or cylinder

Re: [gmx-users] addition of hydronium ion in simulation box

Regarding CpHMD methods, I would just like to add that you have, in fact, several options. In case you are interested, there is a good summary on subject @ http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation. Regards, On 22 September 2015 at 06:59, Groenhof, Gerrit

Re: [gmx-users] Solvating in a solvent other than water

Ah, yes! I hadn't made the molecules whole. It works just fine now. Thank you guys, especially Justin for having pointed out the fault. -Pallavi Banerjee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

On 22/09/15 07:42, Naba wrote: Thank you Justin. I have to deduce some inference from this figure. Please make me out about the following queries. On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul wrote: On 9/21/15 4:00 AM, Naba wrote: Dear Gromacs users and Developers, I

[gmx-users] Free energy perturbation with hamiltonian replica exchange (FEP - HEX)

Dear Gromacs Users, I am running relative binding free energy calculations with free energy perturbations (FEP) but the lambda points do not converge within 10ns of simulation time so I am thinking of using hamiltonian replica exchange (HEX, HREX or H-REMD) with FEP as described in this paper

Re: [gmx-users] backward.py script

Hi Juan, Unfortunately... not yet. But if you're interested, contact me off-list and let's see what we can do :) Cheers, Tsjerk On Tue, Sep 22, 2015 at 2:41 PM, Juan Munoz-Garcia < juan.munoz-gar...@bioch.ox.ac.uk> wrote: > Dear all, > > I’m using the backward.py script to convert CG to

[gmx-users] SDF problem

Dear gromacs user My system consist of 1 molecule + 1000 of solvents (water) in cubic box. I did 5 ns NPT equilibration and currently I am doing analysis stuff such as RDF, density, viscosity, etc. And now I want to try using g_spatial but I stuck on it. I would like to know if you can help me

[gmx-users] backward.py script

Dear all, I’m using the backward.py script to convert CG to atomistic representation. However, to my knowledge (and testing) it only works for 1 frame .gro or .pdb files. Is there any way to make it working for a trajectory in either .gro or .pdb format? Regards. Juan C. Munoz-Garcia --

[gmx-users] distance dependent energy

Dear Gromacs users, I would like to work out the energy (total and kinetic) as a function of the distance from the center of mass of a droplet. However, using g_energy just gave me the values as a function of time. Could anyone tell me the way to get the distance dependent values? Thank you very