[gmx-users] Distance restraints at topology file between gromacs-5.1.4 and gromacs-2018.4

Hi, Gromacs users and developers Actually, I used distance constraint for each chain.itp file. (for example, I added following for chainA.itp /chainB.itp/chainC.itp and so on [distance_restraints] ; i j ? label funct lo up1 up2 weight 155 1762

[gmx-users] Shell platform for GROMACS on Windows?

Hello GROMACS users, To run GROMACS on Windows OS, what is the best shell interface? Cygwin? or anything else? Thank you, Neena -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 177, Issue 12

On Mon, Jan 7, 2019 at 7:07 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit >

[gmx-users] Comparison of PMF profiles in different states of a protein

Hi I am studying the movement of a molecule in two different states of a protein. To do so, I want to calculate a PMF profile in each state using umbrella sampling. My reaction coordinate is the distance between the center-of-mass of a fixed residue and the center-of-mass of the molecule. My goal

Re: [gmx-users] Restarting a simulation: failed to lock the log file

> On 7. Jan 2019, at 11:55, morpheus wrote: > > Hi, > > I am running simulations on a cluster that terminates jobs after a hard > wall clock time limit. Normally this is not a problem as I just restart the > simulations using -cpi state.cpt but for the last batch of simulations I > got (for

Re: [gmx-users] gmx hbond

You could use gmx select to create an index file containing water molecules obeying these criteria at each time-step, and then use gmx hbond for for each index (being sure to only look at the relevant frame only). Something like this: gmx select (your commands here to generate an index index

[gmx-users] delete non-protein atoms in md trajectory

How to convert topol.top (topology file) to psf and trajectory file xtc to dcd in gromacs18? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Restarting a simulation: failed to lock the log file

Hi, I am running simulations on a cluster that terminates jobs after a hard wall clock time limit. Normally this is not a problem as I just restart the simulations using -cpi state.cpt but for the last batch of simulations I got (for most but not all of them) the error: "Failed to lock:

[gmx-users] User defined tabulated potential for a particle with only repulsive interactions, in water

I would like to simulate a particle that has only a repulsive (no attraction) terms in its potential energy interaction with all other particles. I am simulating this particle in tip3p water. I am trying to use the tabulated potential option since I know its potential form, and force as well.