[gmx-users] (no subject)

I am trying to do the molecular dynamics of DNA-ligand complex. I made the ligand files using antechamber and converted the amber files to .gro and .top using acpype.pl. Then I made the complex.gro. when I am trying to run grommp ions.mdp and em.mdp, it gives error saying the following Command

[gmx-users] Spatially resolved diffusion coefficient

Dear GROMACS users, I am interested in obtaining a spatially resolved diffusion coefficient for water in a confined pore system consisting of a slab of metal and water. My goal is to obtain the xy component of diffusion coefficient (parallel to the metal slab) as a function of distance away

[gmx-users] Position restraints with Martini force field

Hi everyone, I am simulating a DNA protein system with Martini forcefield. I want to use position restraints on all DNA atoms. So I used gmx genrestr command to generate .itp file for position restraints of all the DNA atoms. So without including position restraints, my .top file looks like this

Re: [gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

Hi, You might want to take a look at *gmx mindist*, it is capable of counting the number of contacts between the atoms of different groups during any specific period of run. Also you can specify what distance is considered as a contact initiation.

Re: [gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

Hi Hassan, Yes, this is something that I usually do with MDAnalysis, but from experience I've noticed that people are often reluctant to try it. Therefore you could try playing with gmx_select. Something like this should output the number of water oxygen atoms within 5 Å of residue 1 as a

[gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

Dear Gromacs Users I would like to calculate the presence of water molecules number as a function of time, around a ligand during binding to its pocket from a trj.xtc file. How can I do it by Gromacs or any other program? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Interaction energy

Hi I am beginner in MD. Maybe it is not a wise question but i want to calculate the interaction energy between protein and ligand and also PMF in different distances. But i don't know what is the didference between PMF, i mean free energy in particular(by umbrella sampling) and the interaction

[gmx-users] polymer state

Dear all, How can I find the polymer state (monomer, dimer, trimer, ...?) of a protein? I thought it would be the REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT in the pdb file,but for a protein, I read in its article that it is monomer in solution, and this REMARK was HEXAMERIC!!!I need to

[gmx-users] Implementation of drude simulation

Greetings gromacs users, I'm trying to run a simulation of polarizable water and ions with the drude-2013 forcefield. I use the simulation parameters from the supporting information from "Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical

Re: [gmx-users] Gmx distance

To be clear, i put 30 similar AA around NT i want to know how the average distance of group PROTEIN( consist of 30 AA ) varies during 100nS simulation. As i see in .gro file this distance decreased. I mean at the first moment i put them about 3nm far from Z axis of NT. THIS 3NM IS THE MINIMUM

[gmx-users] System Charge in OPLS AA force field.

Hi All, I am working on a system of polymers having both positive and negative charge. I am using OPLS AA force field to wokr on it. While I Vacuum simulated a single chain of the same Charged polymer without any query. After being able to do that I proceeded to Vacuum simulation using 5 chains

[gmx-users] Printing only center of mass of during simulation

Hello Gromacs Users, I wanted to know if there is any way to print only the *centre of mass* of a user defined group(instead of all the x,y,z coordinates) during simulation run (mdrun). I will be really grateful for your suggestions. Waiting for your reply. -- Sudarshan Behera PhD Student

[gmx-users] Third beta release of GROMACS 2019

Hi GROMACS users, The third beta release of GROMACS 2019 is now out and available! As before, we are making the testing versions available for you to be able to get feedback on how well things are working, and what could be improved or if there are any bugs in the code we have missed

Re: [gmx-users] OPLS AA/M error

Dear GMX Users, I am you again for a help with the issue I have encountered as I need to have it solved. If there is anyone who might have any idea of what is going on I would be grateful for contact. I wanted to conduct MD simulations using the newest OPLS-AA force field parameters - OPLS AA/M.