Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

Any suggestions as to how to write the script.? or on feeding the index file to trjconv manually...?? Thank you. [image: Mailtrack] Sender notified by Mailtrack

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

Since gmx trjconv does not work with dynamic selections, you can either feed the index file to trjconv and manually pick which frames to dump or write a script that calls trjconv to dump the atoms you want for each timestep you want. On Thu, Apr 12, 2018 at 10:04 AM, Dilip.H.N

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

The -on option too gives the output as in index format, which i don't want. I want it in a .gro file and not as in an index file format.In gmx select options the output files are written in .xvg/.ndx.dat format only... i want the output to be written like the following:- frame t= 0.000 1543

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

You need -on for gmx select to write out the index file. On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N wrote: > I tried the following two ways ie., with gmx select and with gmx trjorder > > 1) when i give the command :- > gmx trjorder -f nptmd.xtc -s nptmd.tpr -n

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

I tried the following two ways ie., with gmx select and with gmx trjorder 1) when i give the command :- gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell -r 0.35 i got an output file, it has all the water molecules (i have 511 water molecules in my system) for each time

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

You can use either gmx trjorder with the nshell parameter (if it is as simple as within Xnm of Y, use nshell parameter, see manual) or gmx select (if you need some more complex selection). On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N wrote: > Hello all, > > I want to

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

gmx select On Wed, Apr 11, 2018 at 9:54 AM, Dilip.H.N wrote: > Hello all, > > I want to get the water molecules which are at a certain distance (say all > the water molecules which are within 0.35nm of the Nitrogen atom of glycine > molecule). How can i get this all

[gmx-users] Regarding getting the coordinates within certain region of amino-acid

Hello all, I want to get the water molecules which are at a certain distance (say all the water molecules which are within 0.35nm of the Nitrogen atom of glycine molecule). How can i get this all the coordinates.? Any specific commands..?? Thank you. --- With Best Regards, Dilip.H.N PhD