[gmx-users] gmx select

Hi all, I'm trying to work out how many molecules of ligand and water I have within a certain distance. I used the gmx select command below: gmx select -f trajectory.gro -s trajectory.tpr -oi index.dat -select 'resname LIG and within 0.5 of whole_res_com of resnr 1' -dt 100 However, this only

[gmx-users] gmx select help

Hi all, I am running the gmx select command to create a file with all my ligand molecules that are within the cut-off distance specified from the COM of a protein residue as a function of time. Here is the command I am using: gmx select -f traj2.gro -s protein.tpr -dt 100 -on index.ndx

[gmx-users] gmx select

Hi all, I am running the gmx select command to obtain all my ligand molecules that are within a cut-off distance from the COM of a protein residue as a function of time. The output from the command below comes with just the atom positions of my ligand. gmx select -f protein_gly.gro -s

Re: [gmx-users] gmx select with coordinates

Hi Prof. Dan, Thank you very much for the e-mail. How do we define coordinates what we want in VMD Graphical Representation menu? Thank you. On Wed, Oct 10, 2018 at 6:53 AM Dan Gil wrote: > Hi Shan, > > Sorry it's been a while - I don't check this email too often. Did you > figure the

Re: [gmx-users] gmx select with coordinates

Hi Shan, Sorry it's been a while - I don't check this email too often. Did you figure the problem out? I use the Graphical Representations menu of VMD, although I am sure there is a way to do it in the console too. On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com>

Re: [gmx-users] gmx select with coordinates

Dear Prof. Dan, Thank you very much for the suggestion. However, when I gave the command; gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in VMD TkConsole, I didn't get any output. I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90 and y. What could

Re: [gmx-users] gmx select with coordinates

Hi, I believe you are trying to select atoms/particles that are in an infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and (90, 125)? Gmx select uses commands that are similar in syntax to a software called VMD. So I like to use VMD to figure out what I need to give to gmx

Re: [gmx-users] gmx select with coordinates

Dear Gromacs users, I want to make an index files with molecules in a particular area. I have four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which define an area of the system. How can I do it with gmx_select? Can anyone help me? Thank you. On Thu, Sep 27, 2018 at 4:14 PM

[gmx-users] gmx select with coordinates

Dear Gromacs users, I want to make an index files with particular x and y coordinates. There is no restriction for z coordinates. How can I do it with gmx_select? I already tried with the following command. However, it seems I don't get the result I want. gmx select '[45, 90] and [45, 125] and

Re: [gmx-users] gmx select and gmx trjconv or gmx density

Thank you Dr. Abraham! I think I will write a script to do the analysis then. Best Regards, Dan On Mon, Apr 9, 2018 at 12:57 PM, Mark Abraham wrote: > Hi, > > Unfortunately not all tools support dynamic selection groups yet, so the > only useful way to use that

Re: [gmx-users] gmx select and gmx trjconv or gmx density

Hi, Unfortunately not all tools support dynamic selection groups yet, so the only useful way to use that index file is by matching it with the correct single frame from the trajectory, which you might get from e.g. gmx trjconv split Mark On Fri, Apr 6, 2018, 21:37 Dan Gil

[gmx-users] gmx select and gmx trjconv or gmx density

Hi, I am trying to select particles that are z < 20 and z > 10 as a function of time. I think I used gmx select correctly and generated an index file with group names like "(z_<_.8_f2882_t23056.000)" Now I am unsure how I use this index file for gmx trjconv or gmx density. Does anybody have

[gmx-users] gmx select querry

Hello All, I have a question regarding the usage of gmx select. I want to select water molecules in a particular subset in z-direction (example z > 5 and z < 10) for each frame of my trajectory and then carry out analysis using g_mindist on each frame of the trajectory (with selections) For

Re: [gmx-users] gmx select

On 7/13/17 10:01 AM, Pandya, Akash wrote: So I tried with both opening and closing. It seems to select all the molecules in my box which is not what I want. I only want certain glycine molecules that are closest to the protein. May you please suggest another way is which I could achieve

Re: [gmx-users] gmx select

ys.kth.se] On Behalf Of Justin Lemkul Sent: 13 July 2017 14:01 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select On 7/13/17 3:38 AM, Pandya, Akash wrote: > gmx select -f output.gro -select "Close to protein" resname Glyci and within > 0.5 of group "Protein"' &

Re: [gmx-users] gmx select

Justin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 13 July 2017 00:04 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, Can you please copy, paste and

Re: [gmx-users] gmx select

: 13 July 2017 00:04 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes. Mark On We

Re: [gmx-users] gmx select

gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 12 July 2017 22:42 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx select > > Hi, > > What are the residue names in your coordinate file? Glyci probably doesn't > fit >

Re: [gmx-users] gmx select

...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 12 July 2017 22:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pan

Re: [gmx-users] gmx select

Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash wrote: > Hi all, > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > I tried both of these commands I

[gmx-users] gmx select

Hi all, I am trying to select all the glycine molecules with 0.5nm of my protein. I tried both of these commands I got from the gromacs website: gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb gmx select -f output.xtc -s output.tpr

[gmx-users] gmx select

Dear all, I am a little bit lost with the use of select. I am looking at a protein in a water:glycerol mixture. I would like to count how many glycerol molecules there are within 3Angstrom of the protein. I first used the following command to count the central atom (named C2): gmx select -s