Hello everyone
I am looking for a sample Gromacs script and a Plumed file with Distance
Colvar. Please send me one if feasible.
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Cheers
Peter
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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
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} {i
> 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
> &g
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 option
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 bet
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 ca
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 s
Hello everyone
Can someone please send me mailing list addresses where I could get updates
on Postdoctoral positions available in the field of simulations.
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Cheers
Peter
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