[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

Re: [gmx-users] How to add water molecules one by one into the polymer system

They sound like the most appropriate method, if understanding your goal correctly. Write your own script (your favourite, doesn't matter which language) that uses insert-molecules, updates .top, runs grommp, runs simulation, then repeats the cycle 500 times. On Thu, 23 May 2019, 8:10 pm

Re: [gmx-users] Pressure coupling problem

Would be a good idea to test with the latest release, and also create a Redmine with the issue, including the files that generate the problem. On Fri, 24 May 2019, 3:23 am Tam, Benjamin, wrote: > Dear all, > > To follow through with this email. It seems like the barostat problem > comes from a

Re: [gmx-users] wrong trajectory resolution gromacs-2018

Can you post somewhere the contents of the mdout.mdp file? Then we can see the step since, frequency etc that was actually used. On Fri, 24 May 2019, 9:25 am Leigh M, wrote: > I have an mdp file that specifies I want to save coordinates every 10 ps. > > However I'm getting this output that says

[gmx-users] wrong trajectory resolution gromacs-2018

I have an mdp file that specifies I want to save coordinates every 10 ps. However I'm getting this output that says I have an 8 ps trajectory: command 1: gmx check -f 4000t4048.xtc output 1: ^MReading frame 1 time 4008.000 ^MReading frame 2 time 4020.000 Timesteps

[gmx-users] von Mises stress-strain curve

I’m running GROMACS to simulate a simple phospholipid bilayer membrane (POPC) under deformation, and plot the von Mises stress-strain curve to determine yielding point. I have got the membrane deformed and tried to get the stress-strain curve by extract output pressure from .edr file (option

Re: [gmx-users] Pressure coupling problem

Dear all, To follow through with this email. It seems like the barostat problem comes from a different version. As I tested with version gromacs/2016.3/intel-2017-update1, the system remains stable for 1 ns and the same system explode with gromacs/2018.3/intel-2018. Was there some kind of

Re: [gmx-users] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

Hi Mark, Thank you very much for your answer. I have read the GROMACS manual and other documents but still confused, but your explanation make it clearer now. About the pressure coupling, in GROMACS Manual it is said that "In most cases Parrinello-Rahman barostat would be combined with the

[gmx-users] Gyration tensor

Calculate the radii of gyration about the principal axes. Dear all, The -p flag in gmx gyrate would calculate the radii of gyration about the principal axes, Rga, Rgb and Rgc. I wonder what the relation between the eigenvalues of diagonalized gyration tensor and what we get here in Gromacs as

[gmx-users] gmx trjconv

Dear GMX user, I have a 110 GB trajectory from which I would like to extract only the trajectory of the part of my interest, the rest is water. To do so, I use " echo 1 | mpiexec_mpt -n 1 gmx_mpi trjconv -f tot.xtc -s topol.tpr -o nonwater.skip4.xtc -skip 4". The extracting goes very slow

[gmx-users] Pressure coupling problem

Dear Gromacs user, Currently, I am baffled about a simulation that I am running and I hope I will find some answer here. Initially, I have run my system with Berendsen barostat to equilibrate for 1 ns. The system looks fine as there is no box explosion. However, after the equilibration, I

[gmx-users] How to add water molecules one by one into the polymer system

Dear Gromacs users, I have a polymer system and I would like to add water molecules one by one upto 500 water molecules. For instance, after adding a water molecule, I would like to relax/equilibrate the system for 10 ps and again add the molecule and perform the simulation until reaching my

[gmx-users] Tool for energy pair distribution function calculation?

Dear all, I would like to extract an energy pair distribution function for selected atomic pairs in my GMX trajectory. Is there some tool to run this operation? Thank you and Regards, Alessandro -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Tool for energy pair distribution function calculation?

Dear all, I would like to extract an energy pair distribution function for selected atomic pairs in my GMX trajectory. Is there some tool to run this operation? Thank you and Regards, Alessandro -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] control parameter on the Lennard-Jones interactions

Dear Mark, many thanks for your suggestions! Indeed adding of the [ pairtypes ] section seems to solve. Can I asky you which is the difference between [ paitypes ] and [ nonbond_params ] for intramolecular pair interactions? they look very similar: [ pairtypes ] ; i j func V(c6) W(c12)