[gmx-users] a question about surface tension

Hi there, I am doing simulations of a membrane protein, and I am trying to apply surface tension to the membrane in order to observe how the protein respond to it. I have several questions of how to apply a surface tension to a membrane 1, this is what I am using in my mdp file, could

[gmx-users] "Fatal error: Failed to lock: md_0_1.log. Already running simulation?"

Hello everyone I am trying to continue a simulation that hit the walltime: gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt -maxh 96 -deffnm md_0_1 But everytime I am getting this error: "Fatal error: Failed to lock: md_0_1.log. Already running simulation?" I tried the solution in this post without

[gmx-users] Polymer topology and MD Gromacs

Alex, Thanks for your feedback. So far the critters seem to be compliant, align when they should with H bonding, crumple when they should, and grommp’s major complaint is when I forget to adjust the number of residues. But I am unseasoned in MD and following the discussions on gmx-users

[gmx-users] pulling in opposite direction

Dear all. How it is possible to pull reference group as well as pull group using gromacs protocol simultaneously in opposite direction using umbrella protocol of pulling. So far non of the Gromacs expertise have given the answer of this question. Hoping from response . -- *With

Re: [gmx-users] force field not found

Alex, Justin, I've managed to make and run polymers using Avogadro ,modifying the n2t, then creating the top using x2top under 54a7 ff. The method may be useful for others but before presenting it to the user group, it should be reviewed so that glaring mistakes/concepts are revised.

[gmx-users] Average pressure in CG simulation of oil-water system at NAPzT ensemble

Dear All, I am running a coarse-grained martini (elastic network) simulation at NAPzT ensemble for an oil-water system containing a protein at the interface using GROMACS-5.1.4. The system has overall 27,000 atoms including refined polarizable (v2.2refPOL) water molecules (The Journal of Chemical

Re: [gmx-users] force field not found

I don't really work much with small organics or polymers (angle descriptions should be quite important there), so my review would be at the level of what the good old grumpy robot grompp already does. If you are sure of the parameters and your tests are coming out okay, given some criteria, I

[gmx-users] gmx_d energy output at multiple time points?

Hi, When you run "gmx_d energy", by default it prints summary statistics (drift of total energy is what I am most interested in) for the whole run. You can set a time window to analyze using the -b and -e switches. But, is there any way to have it output the statistics for multiple windows? For