Re: [gmx-users] Multisite ion of Mg in Gromacs

Dear all, Could anyone can please help me clarify the last paragraph on page 393 of gromacs manual 2019.1? "when sigma and epsilon need to be supplied (rule 2 and 3), it would seem it is impossible to have non-zero C12 combined with a zero C6 parameter. However, providing a negative sigma will do

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 64

Hello Azadeh For the calculations of the EDP you have to take into account of the charges of the atom (it is mentioned at the end of density tool ("known issue")) . So modify the number of electrons to have the "real" electron numbers in you electron.dat file accordingly. HTH

Re: [gmx-users] Pressure coupling problem

Hi Ben, Could you try your simulation on another GROMACS build (on a different machine perhaps) to isolate the functional cause of your symptoms? Or perhaps use another FF on the same structure? I think this would be of interest to many users. Best wishes, Gregory On 5/25/2019 5:33 AM,

Re: [gmx-users] RMSD for specified length of DNA aptamer

Hi, You should create an index file (use gmx make_ndx) that contains a list of the atom you want to perform RMSD calculation on, e.g P atoms, or whatever you want. Then when you run gmx rms, you have to pass the index file from the above step Best, On Sat, May 25, 2019 at 11:41 AM mmousivand93

[gmx-users] Calculating electron density profile of a lipid bilayer system

Dear Gromacs users I am trying to calculate the electron density profiles of a lipid bilayer system. However I am not getting the correct profile. I would appreciate it a lot if you can help me. Following is the procedure I go through: 1- first I create a ndx file to select the resnames: gmx

[gmx-users] Use of index file generated by gmx select

Hello, I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps interval. I am using gmx select to generate a index.ndx of 25 index for water molecules within 0.5nm of the protein. I want to know how to use this index.ndx file for my calculation - For example: a) If I want to

[gmx-users] RMSD for specified length of DNA aptamer

Dear all I have been run molecular dynamic simulation between DNA(50bp)and small ligand,how to calculate RMSD value for specified length of DNA during 50ns simulation(for example residues from 12 to 25)? Best Regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Pressure coupling problem

Hi Jacob, Thank you for your responses. My system is set up for generating a polymer with over 40800 atoms. So initially, I need to simulate the system in different pressure in order to set up a "correct" simulation system. I have simulated with Berendsen barostat for 10 ns and through the