Re: [gmx-users] Question on energygrps setting

Devargya Chakraborty On Thu 7 May, 2020, 8:23 PM Justin Lemkul, wrote: > > > On 5/7/20 10:49 AM, Devargya Chakraborty wrote: > > Suppose my system contains an anion a cation and water and I have done an > > nvt simulation.after the completion I want to see the energy profile of

Re: [gmx-users] Question on energygrps setting

Suppose my system contains an anion a cation and water and I have done an nvt simulation.after the completion I want to see the energy profile of the individual groups like the cation or the anion etc. Can anybody guide me how to use the energy grps option in analysing that. Thanks Devargya

Re: [gmx-users] Replicate a structure

> > Gmx editconf you can use with -translate flag...after that merz the > > coordinates of two water droplets. I hope this may help you. > > > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < > > devargyachakraborty@gmail.com> wrote: > >

[gmx-users] Replicate a structure

I have an equilibrated droplet of water. What I want to do is replicate that droplet in the x direction. So that my simulation box will carry two water droplets. Is that possible in gromacs. If yes please guide me. Thank you Devargya Chakraborty -- Gromacs Users mailing list * Please search

[gmx-users] error on graphene sheet simulation

while going through your tutorial on graphene sheet i was facing an error. https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ NOTE 2 [file nvt.mdp]: The Berendsen thermostat does not generate the correct kinetic

Re: [gmx-users] problem while calculating order parameter

Thanks On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul wrote: > > > On 2/15/20 4:50 AM, Devargya Chakraborty wrote: > > i want to calculate the order prameter between two carbon atom namrd C01 > > and C03 in my topology file but while calculating, i am getting the > > fol

[gmx-users] problem while calculating order parameter

i want to calculate the order prameter between two carbon atom namrd C01 and C03 in my topology file but while calculating, i am getting the following error. Taking z axis as normal to the membrane Reading file nvt.tpr, VERSION 2019.1 (single precision) Using following groups: Groupname: System

[gmx-users] simulation on graphite sheet

Hello, I was thinking of simulating a liquid on graphite surface and have made a system but couldnt simulate it. while doing the nvt simulation, after some time i am getting lincs error. can anybody help me, if you want i can send you the files. Thanks, Devargya chakraborty PhD scholar

Re: [gmx-users] cant compute msd

ual > molecule a diffusion constant is computed for its center of mass. The > chosen > index group will be split into molecules." > > > Best, > > Christian > > > On 2020-01-08 11:12, Devargya Chakraborty wrote: > > hi, when i am using the command > &g

[gmx-users] cant compute msd

hi, when i am using the command gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg after that choosing a group the following line is coming. Select a group to calculate mean squared displacement for: Group 0 ( System) has 5616 elements Group 1 ( Other) has 5616

[gmx-users] Fwd: setting ionic liquid simulation in gromacs

-- Forwarded message - From: Devargya Chakraborty Date: Thu, 19 Dec 2019 at 18:17 Subject: setting ionic liquid simulation in gromacs To: can any body guide me or tell me the steps for the simulation of ionic liquid and how to properly use the .itp files available

[gmx-users] my mail id

devargyachakraborty@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit