[gmx-users] Request for Plumed sample scripts

Hello everyone I am looking for a sample Gromacs script and a Plumed file with Distance Colvar. Please send me one if feasible. -- Cheers Peter -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Output trajectory frames as separate coordinate files

My apologies, this can be achieved easily with the command below: gmx trjconv -s -f -n -split -o . On Thu, Feb 20, 2020 at 2:15 PM Peter Mawanga wrote: > Hello everyone > > Is it possible to output different frames of a .trr trajectory as single > .gro files without supply

[gmx-users] Output trajectory frames as separate coordinate files

Hello everyone Is it possible to output different frames of a .trr trajectory as single .gro files without supplying an index (.ndx) file each time? In VMD this can be achieved with: set mol [molinfo top] set sel [atomselect $mol all] set n [molinfo $mol get numframes] for {set i 0} {$i < $n}

Re: [gmx-users] Selective RMSD calculation

You can calculate the rmsd by passing the index file of the ligand... > gmx rms -h > > On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, > > wrote: > > > Hello everyone > > > > After fitting the protein-ligand system to the starting conformation, I > >

[gmx-users] Selective RMSD calculation

Hello everyone After fitting the protein-ligand system to the starting conformation, I would like to extract the RMSD information for the ligand only but cannot find such an option for a selective output. Please let me know if this can be achieved with the gmx tool, I couldn't find such an

[gmx-users] Protein-Ligand Interaction calculation

Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file. Hence I am not able to calculate the energy

Re: [gmx-users] Experimental to Simulation Time Period Conversion

Thanks a lot sir for your reply. Since experiments take place over hours but the simulations can at best approach millisecond levels. I was wondering if there is an acceptable time conversion factor from experiments to simulations. For example, the simulation data generated over a 350 ns period

[gmx-users] Experimental to Simulation Time Period Conversion

Dear group members My sincere apologies for the non-Gromacs related question, but I require this information urgently and hence posted my query here. Could someone please provide me with any guidelines to appropriately model experimental processes with molecular dynamics simulations? Since the

[gmx-users] Mailing list for Postdoctoral opportunities in Simulations

Hello everyone Can someone please send me mailing list addresses where I could get updates on Postdoctoral positions available in the field of simulations. -- Cheers Peter -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List