Re: [gmx-users] Potential energy reported by gmx energy command

If I am not wrong, you are suggesting the "per mol" in KJ/mol is total number of particles in the system. Which in special case for pure component system should give per particle energy scaled by Avogadro number, so for my case the RMSD decrease by (N)^1/2 should come out to be same whether I

Re: [gmx-users] [EXT] Re: 500ns simulation

Hi Raag, Within your .mdp file there is a "Run parameters" section that has the following line items (see below). If you want to achieve 500 ns you need to increase the nsteps and multiply it times the timestep - ensuring that the timestep is appropriate enough for what you want to achieve.

Re: [gmx-users] HIS as HID or HIE

On 7/5/18 8:50 AM, antonia vyrkou wrote: Hello, I am using GROMACS 5.1.4 and while trying to convert a .pdb file to .gro I get the error message “Fatal error: Atom HD1 in residue HIS 66 was not found in rtp entry HIE with 17 atoms while sorting atoms.” Is it not possible to treat some

[gmx-users] gmx rms vs. trjconv

I ran into what seems to be a bug, namely that the -skip option in gmx rms doesn't seem to do anything. The output always has the RMSD values for all frames, even if -skip is specified. I filed a bug (https://redmine.gromacs.org/issues/2565). Then I resorted to trjconv to do the skipping

[gmx-users] Is any plan to implement the energy group exclusions for verlet cutoff scheme

Dear Gromacs developers For the latest Gromacs version (GROMACS 2018.2) available, energy group exclusions do not support by the verlet cutoff scheme (The group cutoff scheme supports the energy group exclusions,but it is inconvinent to use). So is there a time table when energy group

[gmx-users] HIS as HID or HIE

Hello, I am using GROMACS 5.1.4 and while trying to convert a .pdb file to .gro I get the error message “Fatal error: Atom HD1 in residue HIS 66 was not found in rtp entry HIE with 17 atoms while sorting atoms.” Is it not possible to treat some HIS molecules as HID (where HD1 exists) and

[gmx-users] rerun from random seeds

Hi Gromacs folks, I am trying to re-run a 100 ns simulation with different velocities and random seed. Would the setup from the mdp file as the following a good one? ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature

[gmx-users] how to reassign velocities in the .mdp file effectively?

Hi Gromacs folks, I am trying to test the reproducibility of the md production run. Should I use the product from the previous MD run as the starting structure and run it with the same mdp files, or just simply do a re-run with all the same mdp files from the original pdb file? Thanks in advance,

[gmx-users] gmx rms vs. trjconv

Never mind my previous question about using trjconv for fitting in RMSD calculations. It does produce identical results compared to using gmx rms alone. I just had a subtle error in atom numbering, which resulted in bogus RMSD values. -- Gromacs Users mailing list * Please search the

[gmx-users] Queries regarding temperature gradient

Dear all, I am setting up a system where I want the solute to be immersed in a solvent with a temperature gradient. I have defined two different temperature groups, two portions of the solvent, and want them to be at say T1 and T2 kelvins. The rest of the system will not be subjected to a

Re: [gmx-users] how to reassign velocities in the .mdp file effectively?

I am trying to test the reproducibility of the md production run. You can use the options gen-vel = yes gen-temp = 300 gen-seed = -1 in your .mdp file and run again. That example will generate new random velocities corresponding to 300 K and

[gmx-users] Tacticity in polymer simulation

Hi everyone, How does one go about preparing a polymer in a given state of tacticity? >From what I understand about tacticity in polymers, it boils down to coefficients(C1,C2,C3,C4,C5,C6) in Ryckaert-Bellemans function. If the potential well is not deep enough, the polymer can easily transition