Hi,
On Wed, Dec 21, 2022 at 9:11 PM Swapnil Singh via AMBER
<amber.ambermd.org> wrote:
>
> Hello,
> I am trying to sort the frames based on my RDF output. In the RDF I can see
> two conformations at a distance of 4-8 A and another at 8-10 A so I want to
> see those frames so that I can visualize those conformations. I am able to
> use the filter command for distance but can not use it for RDF as I cannot
> name anything after radial (also attached distance command that worked
> well). Can someone please help me out with this?
So the issue here is that the radial distribution function is really a
histogram, but you're trying to use it as a time series. If all you
want is to extract the frames where the distance between :108.N1
:39.CG ranges from 4 to 8 Ang. you would do something like:
parm myparm.parm7
trajin mytraj.nc
distance d1 :108.N1 :39.CG
filter d1 min 4 max 8
trajout traj.n1.cg.4.8.nc
If you want to do multiple output trajectories in a single pass you
could use the 'maxmin' keyword of 'outtraj' instead:
parm myparm.parm7
trajin mytraj.nc
distance d1 :108.N1 :39.CG
outtraj traj.n1.cg.4.8.nc maxmin d1 min 4 max 8
outtraj traj.nc.cg.8.10.nc maxmin d1 min 8 max 10
Hope this helps,
-Dan
>
>
>
>
>
>
>
> *#filter RDFparm CaM_solv.prmtoptrajin CaM_solv_equil.nc 1 last 1radial out
> 108-39.dat 0.1 15.0 :108.N1 :39.CG filter min 3.0 max 8.0 out filter.dat
> outtraj distance1-filtered.nc <http://distance1-filtered.nc> netcdf go*
>
> parm CaMCNFiNOSout_solv.prmtop
> trajin CaMCNFiNOSout_equil.nc 1 last 1
> dihedral D :108.CA :108.CB :108.C2 :108.C3 out torsion.dat
> filter D min 80.0 max 90.0 out filter.dat
> outtraj distance1-filtered.nc netcdf
> go
>
>
>
> Thanks,
> Swapnil
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Received on Thu Dec 22 2022 - 07:30:02 PST
