[gmx-users] g_spatial Problem

Dear Sakiru: This topic was discussed before on-list: https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=subject:%22%5Bgmx-users%5D+g_spatial%22=newest=1 Basically, if you have 48 molecules of A, then you need to process your trajectory so that it is 48x larger in

[gmx-users] g_spatial Problem

Hi everyone, I want to generate the spatial distribution function of Molecule A around molecules B. I have 48 molecules of A and 200 molecules of B in a cubic box and I want to find the spatial distribution of B around A in the first shell of B ( about 5A away from A

Re: [gmx-users] g_spatial Problem

" representation is kind of useless. I will send you an image of the SDF that I generated off list. Good luck, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Rubaiyet Ab

Re: [gmx-users] g_spatial Problem

kth.se> on behalf of Rubaiyet > Abedin <abedi...@husky.neu.edu> > Sent: 04 October 2016 23:45:31 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] g_spatial Problem > > Dear Dr. Neale, > > Thanks for your reply. Actually my system is quite a big system. It > c

Re: [gmx-users] g_spatial Problem

> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Rubaiyet > Abedin <abedi...@husky.neu.edu> > Sent: 26 September 2016 13:18:46 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] g_spatial Problem > > Dear Sir, > > Hope y

Re: [gmx-users] g_spatial Problem

26 September 2016 13:18:46 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_spatial Problem Dear Sir, Hope you are doing good. I am working with a system that contains ionic liquid and refrigerant. To avoid complication let’s say my system contains the following: Cation (1) Anion (2)

[gmx-users] g_spatial Problem

Dear Sir, Hope you are doing good. I am working with a system that contains ionic liquid and refrigerant. To avoid complication let’s say my system contains the following: Cation (1) Anion (2) Type A (3) Type B (4) And the system (0). I want to get the spatial distribution function of type

[gmx-users] g_spatial problem

Dear Sir, Hope you are doing good. I am working with a system that contains ionic liquid and refrigerant. To avoid complication let’s say my system contains the following: Cation (1) Anion (2) Type A (3) Type B (4) And the system (0). I want to get the spatial distribution function of type

[gmx-users] g_spatial

I am simulating an ionic liquid, and I want to generate a spatial density map on the anion around the cation. I want an image that looks like this:

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

Dear sir, congrats..and thank you very much for your kind replys.. I fitted some group also I tried whatever possible ways 1.water and water oxygen 2.groups and total system also Even that group and SDF space

[gmx-users] g_spatial: merging solvent ond solute:::need some distance

g_spatial Use make_ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run g_spatial on the .xtc output of step #3. 5. Load grid.cube into VMD and

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

http://gromacs.5086.x6.nabble.com/file/n5013540/OH.jpeg I meen after g_spatial calculation done. visualisation problem coming. molecule and SDF surface are overlapping somewhat . why? is this wrong result -- View this message in context:

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

http://gromacs.5086.x6.nabble.com/file/n5013541/OH.jpeg I meen after g_spatial calculation done. visualisation problem coming. molecule and SDF surface are overlapping somewhat . why? is this wrong result -- View this message in context:

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx EOF 6 7 EOF g_spatial

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

-users] g_spatial: merging solvent ond solute:::need some distance g_spatial Use make_ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx EOF 6 7 EOF g_spatial