[gmx-users] g_spatial Problem

[Christopher Neale]

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 which 48 copies each have a different 
molecule of A placed first, then all these 48 segments are concatented together 
and you make the SDF around not the entire A group, but only the first instance 
of A.

To generate only the SDF of the first shell of B is a little harder and 
requires either ordering of a fixed number of closest B molecules (different 
for each frame, but can be done on the 48x trajectory after the procedure noted 
above).

There is *a lot* of processing before hitting gmx sdf for what you want to do, 
and perhaps mdanalysis or loos or some other third party anaysis tool can do 
this out of the box for you — it’s worth checking.

You should also see the noted in an other SDF comment I posted earlier today. 
Centering with PBC wrapping are going to be important in your preprocessing 
steps.

To address a couple of your other sub-questions:
- g_spatial does not do fittings, you do them beforehand (which was intended to 
maximize flexibility of the tool). However, if you have 48 free floating 
molecules of A and you fit on them and make an SDF of B then you should just be 
getting random noise, so either (a) pick a single A to fit on and make the SDF 
of all B (correct, but 48x less data) or use the concatenation procedure above 
and again fit only on a single molecule of A.
- rotation and translation are intended to be done on the entire system, so 
both groups plus everything else... this is in the trjconv steps, not g_spatial.
- everything in trjconv or g_spatial is done on all frames unless you use -b -e 
options to specify not to.

Chris.

— original message —

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 based on RDF).
I have followed the steps in the manual and the output does not give a clear 
picture of what I want to see.
I have a couple of questions:
- Does g_spatial do fittings and analysis on one of the 48 molecules or its 
averaged?

- How can I select only the region close to molecule A if want to?

- Are the rotation and translation done on both groups as the central molecule 
was outside the sphere of B generated?

- Is it done on all the frames?
Your help is highly appreciated.

Thank you very much.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] g_spatial Problem

[Badmos, Sakiru]

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 based on RDF).
I have followed the steps in the manual and the output does not give a clear 
picture of what I want to see.
I have a couple of questions:
- Does g_spatial do fittings and analysis on one of the 48 molecules or its 
averaged?

- How can I select only the region close to molecule A if want to?

- Are the rotation and translation done on both groups as the central molecule 
was outside the sphere of B generated?

- Is it done on all the frames?
Your help is highly appreciated.

Thank you very much.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] g_spatial Problem

[Christopher Neale]

This works for me (careful with line wrapping if this email or the list mangles 
it):

#!/bin/bash

PATH=/project2/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.7/exec/bin:$PATH
export 
GMXLIB=/project2/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.7/exec/share/gromacs/top

# setup variables
CENTRAL="CHO"
SDF="CHL"
top=topology.top
gro=bath_298K.part0001.gro
xtc=bath_298K.part0001.xtc

# generate a .tpr file because one was not provided in the tarball
cp itp\ files/* .
rm -f this.tpr mdout.mdp
touch empty.mdp
grompp -f empty.mdp -p $top -c $gro -o this.tpr -maxwarn 1

# make the index file
clist=$(grep $CENTRAL $gro|awk '{print $1}'|sed "s/$CENTRAL//"|uniq)
{
  for i in $clist; do
echo "r $i"
echo "r $i || \"$SDF\""
  done
  echo q
} > my.input
rm -f index.ndx
cat my.input | make_ndx -f $gro -o index.ndx

# create the independent segments
mkdir -p BITS
for i in $clist; do
  rm -f BITS/central_${i}.xtc
  echo -e "r_${i}\nr_${i}_${SDF}\n"| trjconv -f $xtc -s this.tpr -o 
BITS/central_${i}.xtc -pbc atom -center -n index.ndx
done

# join the segments
rm -f tot.xtc
trjcat -f $(for i in $clist; do echo -n "BITS/central_${i}.xtc "; done) -o 
tot.xtc -cat -nosort -keeplast

# create a gro for the new file type
i=$(echo $clist|head -n 1|awk '{print $1}')
rm -f onecentral.gro
echo -e "r_${i}\nr_${i}_${SDF}\n"| trjconv -f $gro -s this.tpr -o 
onecentral.gro -pbc mol -center -n index.ndx

# make a new .ndx file
rm -f index2.ndx
echo q | make_ndx -f onecentral.gro -o index2.ndx

# process this trajectory for fitting
rm -f tot_fitted.xtc
echo -e "${CENTRAL}\nSystem\n" | trjconv -f tot.xtc -fit rot+trans -s 
onecentral.gro -pbc none -n index2.ndx -o tot_fitted.xtc

## make the SDF
rm -f grid.cube
echo -e "${SDF}\n${CENTRAL}\n" | g_spatial -f tot_fitted.xtc -s onecentral.gro 
-nab 100

## Run VMD. Load grid.cube as isosurface and onecentral.gro to show your 
choline.
## Note the ability to use surface or grid representations for the isosurface. 
The "points" 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 
Abedin <abedi...@husky.neu.edu>
Sent: 05 October 2016 15:58:14
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_spatial Problem

Dear Dr. Neale,

Please find the following link of dropbox that contains the files.

https://www.dropbox.com/sh/ifeaegequznnbgg/AABO9AzE3PrbNtGfgMike0tWa?dl=0

Please let me know if you need anything else. I really appreciate your help.

Rubaiyet

On Wed, Oct 5, 2016 at 1:01 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> sent a reply previously, but looks like it was lost on my end.
>
> make a tarball of .gro .top all .itp and a small .xtc (5 frames) and post
> it somewhere and put a link on this list. Add a description of which
> molecule you want for central solute and what you want to make the SDF for.
> I will then take a look and post a script to make the SDF.
>
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.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
> contains:
>
> Cation - 250 molecules
> Anion - 250 molecules
> Type A  (urea)- 500 molecules
> Type B (refrigerant)- 250 molecules
>
> I want to get spatial distribution function like the following. I used this
> picture as because this system is similar to mine:
> https://s26.postimg.org/hmw56k5d5/demo.jpg
>
> Let's say I am trying to get the sdf of anions around the cation (solute).
> When I am going through the manual of g_spatial, it did not specify I have
> to choose a single atom of solute. So first I took all the molecules of
> cation as a centered group and followed the steps that I mentioned in the
> earlier mail. I got something like this:
> https://s26.postimg.org/4794h3wvd/image.jpg
> If I load both grid files, it turned out like this :
> https://s26.postimg.org/hpg0te90p/image.jpg
>
> First of all it's rectangular, and all the sdf that I saw in the paper are
> spherical and in the center there are only one molecule (which is clearly
> different from mine).
>
> In the forum, I read that there should be only one centered molecule. So I
> made an index file including a random molecule of Cation and followed the
> steps. This time I got the image like thi

Re: [gmx-users] g_spatial Problem

[Rubaiyet Abedin]

Dear Dr. Neale,

Please find the following link of dropbox that contains the files.

https://www.dropbox.com/sh/ifeaegequznnbgg/AABO9AzE3PrbNtGfgMike0tWa?dl=0

Please let me know if you need anything else. I really appreciate your help.

Rubaiyet

On Wed, Oct 5, 2016 at 1:01 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> sent a reply previously, but looks like it was lost on my end.
>
> make a tarball of .gro .top all .itp and a small .xtc (5 frames) and post
> it somewhere and put a link on this list. Add a description of which
> molecule you want for central solute and what you want to make the SDF for.
> I will then take a look and post a script to make the SDF.
>
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.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
> contains:
>
> Cation - 250 molecules
> Anion - 250 molecules
> Type A  (urea)- 500 molecules
> Type B (refrigerant)- 250 molecules
>
> I want to get spatial distribution function like the following. I used this
> picture as because this system is similar to mine:
> https://s26.postimg.org/hmw56k5d5/demo.jpg
>
> Let's say I am trying to get the sdf of anions around the cation (solute).
> When I am going through the manual of g_spatial, it did not specify I have
> to choose a single atom of solute. So first I took all the molecules of
> cation as a centered group and followed the steps that I mentioned in the
> earlier mail. I got something like this:
> https://s26.postimg.org/4794h3wvd/image.jpg
> If I load both grid files, it turned out like this :
> https://s26.postimg.org/hpg0te90p/image.jpg
>
> First of all it's rectangular, and all the sdf that I saw in the paper are
> spherical and in the center there are only one molecule (which is clearly
> different from mine).
>
> In the forum, I read that there should be only one centered molecule. So I
> made an index file including a random molecule of Cation and followed the
> steps. This time I got the image like this:
> https://s26.postimg.org/7gs51bacp/25percent_Copy.jpg
>
> So I am not sure what I am doing wrong. I tried to look for help. But I
> could not find any till now. Right now I am completely stuck.
>
> The process you said- to make 10 separate trajectories, in my case there
> are 250 molecules of solute and I have to do 250 analysis and then
> concatenate all the trajectories? I am not clear about this. I have
> completed my simulation, I have the  final trjectory and gro file. What you
> are suggesting is to take the trajectory and output it as 1 solute + all
> solvents (anion + type A + type B) and then concatenate all these
> trajectories.  Then run the steps that I enlisted. It is something like
> this?
>
> I am really thankful for your time.
>
> Rubaiyet
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Tue, Oct 4, 2016 at 9:44 PM, Christopher Neale <
> chris.ne...@alum.utoronto.ca> wrote:
>
> > Can you please describe the system a bit more (especially how many
> > molecules of each of the 4 types you have) and also provide more
> > information about what you want to obtain (sdf, obviously, but of what
> and
> > ideally also why).
> >
> > 1. your procedure could be ok, but also maybe not. Depends on what you
> are
> > trying to achieve. I am presuming there is only 1 "anion" though (based
> on
> > the image you sent me off-list) although that doesn't jive with your
> > question #2, so I am confused here. Fitting over multiple "anion"
> molecules
> > that are separately diffusing is not likely what you want -- (B) the
> > grid.cube file is a rectangular matrix, so that is expected. The regions
> > with non-zero density will not fill up the entire rectangle though,
> usually.
> >
> > 2. The g_spatial program is intended for a single central fitting group.
> > There was an old program called g_sdf that may (or may not) do what you
> > want -- it was intended to look at multiple central solutes though as I
> > recall. If you want to have the cumulative sdf over all "anions" then you
> > have to do more processing. What I do in this case is this. Say I have 10
> > "anion" solute molecules (the central group for which you want to build
> an
> > sdf of other molecules around ... I'm going to call this the solute from
> > 

Re: [gmx-users] g_spatial Problem

[Rubaiyet Abedin]

Dear Dr. Neale,

Thanks for your reply. Actually my system is quite a big system. It
contains:

Cation - 250 molecules
Anion - 250 molecules
Type A  (urea)- 500 molecules
Type B (refrigerant)- 250 molecules

I want to get spatial distribution function like the following. I used this
picture as because this system is similar to mine:
https://s26.postimg.org/hmw56k5d5/demo.jpg

Let's say I am trying to get the sdf of anions around the cation (solute).
When I am going through the manual of g_spatial, it did not specify I have
to choose a single atom of solute. So first I took all the molecules of
cation as a centered group and followed the steps that I mentioned in the
earlier mail. I got something like this:
https://s26.postimg.org/4794h3wvd/image.jpg
If I load both grid files, it turned out like this :
https://s26.postimg.org/hpg0te90p/image.jpg

First of all it's rectangular, and all the sdf that I saw in the paper are
spherical and in the center there are only one molecule (which is clearly
different from mine).

In the forum, I read that there should be only one centered molecule. So I
made an index file including a random molecule of Cation and followed the
steps. This time I got the image like this:
https://s26.postimg.org/7gs51bacp/25percent_Copy.jpg

So I am not sure what I am doing wrong. I tried to look for help. But I
could not find any till now. Right now I am completely stuck.

The process you said- to make 10 separate trajectories, in my case there
are 250 molecules of solute and I have to do 250 analysis and then
concatenate all the trajectories? I am not clear about this. I have
completed my simulation, I have the  final trjectory and gro file. What you
are suggesting is to take the trajectory and output it as 1 solute + all
solvents (anion + type A + type B) and then concatenate all these
trajectories.  Then run the steps that I enlisted. It is something like
this?

I am really thankful for your time.

Rubaiyet













On Tue, Oct 4, 2016 at 9:44 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Can you please describe the system a bit more (especially how many
> molecules of each of the 4 types you have) and also provide more
> information about what you want to obtain (sdf, obviously, but of what and
> ideally also why).
>
> 1. your procedure could be ok, but also maybe not. Depends on what you are
> trying to achieve. I am presuming there is only 1 "anion" though (based on
> the image you sent me off-list) although that doesn't jive with your
> question #2, so I am confused here. Fitting over multiple "anion" molecules
> that are separately diffusing is not likely what you want -- (B) the
> grid.cube file is a rectangular matrix, so that is expected. The regions
> with non-zero density will not fill up the entire rectangle though, usually.
>
> 2. The g_spatial program is intended for a single central fitting group.
> There was an old program called g_sdf that may (or may not) do what you
> want -- it was intended to look at multiple central solutes though as I
> recall. If you want to have the cumulative sdf over all "anions" then you
> have to do more processing. What I do in this case is this. Say I have 10
> "anion" solute molecules (the central group for which you want to build an
> sdf of other molecules around ... I'm going to call this the solute from
> here on). Then you make 10 copies of the trajectory in which you only
> output one solute (different one each time) and also include all the
> solvent (this part will be the same in all trajectories). Then concatenate
> all of these trajectories with trjconv -cat -nosort. You may need to create
> a .tpr for this trajectory, or possibly g_spatial will accept a .gro or
> .pdb as input to the -s option. Now you take this concatenated trajectory
> and run it through all the steps that you listed in your email. This should
> give you what you want.
>
> Note: if your solute is flexible, then you may not want to fit on the
> entire solute. That may lead to smearing. I would certainly try it, but I
> would also try fitting on different subsets of the solute (like one charged
> region) that have at least 3 atoms and make that sdf as well.
>
> 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
> 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 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

Re: [gmx-users] g_spatial Problem

[Christopher Neale]

Can you please describe the system a bit more (especially how many molecules of 
each of the 4 types you have) and also provide more information about what you 
want to obtain (sdf, obviously, but of what and ideally also why).

1. your procedure could be ok, but also maybe not. Depends on what you are 
trying to achieve. I am presuming there is only 1 "anion" though (based on the 
image you sent me off-list) although that doesn't jive with your question #2, 
so I am confused here. Fitting over multiple "anion" molecules that are 
separately diffusing is not likely what you want -- (B) the grid.cube file 
is a rectangular matrix, so that is expected. The regions with non-zero density 
will not fill up the entire rectangle though, usually.

2. The g_spatial program is intended for a single central fitting group. There 
was an old program called g_sdf that may (or may not) do what you want -- it 
was intended to look at multiple central solutes though as I recall. If you 
want to have the cumulative sdf over all "anions" then you have to do more 
processing. What I do in this case is this. Say I have 10 "anion" solute 
molecules (the central group for which you want to build an sdf of other 
molecules around ... I'm going to call this the solute from here on). Then you 
make 10 copies of the trajectory in which you only output one solute (different 
one each time) and also include all the solvent (this part will be the same in 
all trajectories). Then concatenate all of these trajectories with trjconv -cat 
-nosort. You may need to create a .tpr for this trajectory, or possibly 
g_spatial will accept a .gro or .pdb as input to the -s option. Now you take 
this concatenated trajectory and run it through all the steps that you listed 
in your email. This should give you what you want.

Note: if your solute is flexible, then you may not want to fit on the entire 
solute. That may lead to smearing. I would certainly try it, but I would also 
try fitting on different subsets of the solute (like one charged region) that 
have at least 3 atoms and make that sdf as well.

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 
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 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
A around Anion. So the central molecule will be the anion. I used the
following commands:



*1.  **make_ndx -f bath_298K.part0001.gro -o bath_298K_index.ndx*



*2.  **trjconv -s bath_298K.tpr -f bath_298K.part0001.xtc -o
bath_298K_b.xtc -center  -ur compact -pbc none  -n bath_298K_index.ndx*



I selected Anion (2) for centering and system (0) for output



*3.  **trjconv -s bath_298K.tpr -f bath_298K_b.xtc -o bath_298K_c.xtc
-fit rot+trans*



I selected Anion (2) for fitting and system (0) for output



*4.  **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and type A (3) to output coordinates



*5.  **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and Anion (2) to output coordinates



I got two grid.cube file and load them into vmd. For the grid.cube (from
step 4) I chose the isosurface value 0.01 and viewed the other cube file as
a single molecule. I have several question:



1.  Do you think I am following the right procedure specially I am
confused and step 4 and 5. After loading both of the grid.cube file I got
something like this the attached.

 For some cases I even got rectangular box. Should it be a sphere?

2.  I am choosing a random Anion (2). Every time I choose a different
anion, I see different cloud shape. I am confused if I am doing something
wrong or I have to choose the central molecule following any specific
technique.


Please help me out with this. Thanks a lot.



Rubaiyet
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] g_spatial Problem

[Rubaiyet Abedin]

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
A around Anion. So the central molecule will be the anion. I used the
following commands:



*1.  **make_ndx -f bath_298K.part0001.gro -o bath_298K_index.ndx*



*2.  **trjconv -s bath_298K.tpr -f bath_298K.part0001.xtc -o
bath_298K_b.xtc -center  -ur compact -pbc none  -n bath_298K_index.ndx*



I selected Anion (2) for centering and system (0) for output



*3.  **trjconv -s bath_298K.tpr -f bath_298K_b.xtc -o bath_298K_c.xtc
-fit rot+trans*



I selected Anion (2) for fitting and system (0) for output



*4.  **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and type A (3) to output coordinates



*5.  **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and Anion (2) to output coordinates



I got two grid.cube file and load them into vmd. For the grid.cube (from
step 4) I chose the isosurface value 0.01 and viewed the other cube file as
a single molecule. I have several question:



1.  Do you think I am following the right procedure specially I am
confused and step 4 and 5. After loading both of the grid.cube file I got
something like this the attached.

 For some cases I even got rectangular box. Should it be a sphere?

2.  I am choosing a random Anion (2). Every time I choose a different
anion, I see different cloud shape. I am confused if I am doing something
wrong or I have to choose the central molecule following any specific
technique.


Please help me out with this. Thanks a lot.



Rubaiyet
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] g_spatial problem

[Rubaiyet Abedin]

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
A around Anion. So the central molecule will be the anion. I used the
following commands:



*1.  **make_ndx -f bath_298K.part0001.gro -o bath_298K_index.ndx*



*2.  **trjconv -s bath_298K.tpr -f bath_298K.part0001.xtc -o
bath_298K_b.xtc -center  -ur compact -pbc none  -n bath_298K_index.ndx*



I selected Anion (2) for centering and system (0) for output



*3.  **trjconv -s bath_298K.tpr -f bath_298K_b.xtc -o bath_298K_c.xtc
-fit rot+trans*



I selected Anion (2) for fitting and system (0) for output



*4.  **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and type A (3) to output coordinates



*5.  **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and Anion (2) to output coordinates



I got two grid.cube file and load them into vmd. For the grid.cube (from
step 4) I chose the isosurface value 0.01 and viewed the other cube file as
a single molecule. I have several questions:



1.  Do you think I am following the right procedure specially I am
confused and step 4 and 5. After loading both of the grid file I got
something like this:



For some cases I even got rectangular box. Should it be a sphere?



2.  I am choosing a random Anion (2). Every time I choose a different
anion, I see different cloud shape. I am confused if I am doing something
wrong or I have to choose the central molecule following any specific
technique.



Please help me out with this. Thanks a lot.



Rubaiyet
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] g_spatial

[Stella Nickerson]

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:

http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53492h-f4.gif

That is, I want the isosurface of the cation right around one anion. The
people who made that image say they used VMD, but I can't figure out how to
do it. I try to use g_spatial, but I get a density map every anion in the
box (a big white cloud. Not useful).

First I ran:

trjconv -s md.tpr -f mdDone.trr -o noPBC.trr -pbc mol -ur compact -center
with the cation as the group to be centered and the entire system as the
output group.

Then I ran:

trjconv -s md.tpr -f noPBC.trr -o fit.trr -fit rot+trans

Then I ran:

g_spatial -f fit.trr -s md.tpr -nab 20

(nab 20 because -nab 10 resulted in a sigmentation fault.)

I also tried making an index file defining exactly one cation as it's own
index group and used that as the solute. That didn't seem to change
anything.

-Stella
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[srinivasa rao lanke]

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 overlapping in VMD view
.
some one suggested g_sdf is fine for this sdf calculation
i am using 4.6.3 version...but g_sdf is not available in this version.


*
IN gromacs manual given one message...

WARNINGS:
The SDF will be generated for a cube that contains all bins that have some
non-zero occupancy. However,
the preparatory -fit rot+trans option to trjconv implies that your system
will be rotating and
translating in space (in order that the selected group does not). Therefore
the values that are returned will
only be valid for some region around your central group/coordinate that has
full overlap with system volume
throughout the entire translated/rotated system over the course of the
trajectory. It is up to the user to ensure
that this is the case*

what is the meaning of these lines from manual ???.







--
View this message in context: 
http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538p5013554.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[srinivasa rao lanke]

 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 view as an isosurface.

I simulated one molecule with water system
1 step i selected solute i.e molecule and totatel system
2 step also same like 1st step
3 step i selected four atoms from molecule and water OW
grid.cube file created and seen in VMD

I am looking for sdf of molecule group and water Oxygen

I am seeing sdf surface and my molecule atoms are overlapping in 3D view

but most of the publication i have seen that there is a distance between sdf
surface and
water oxygen.

Could you please suggest me how to correct this problem.

thank you very much advance


Srinivas
phd student
IIT hyderabad 

--
View this message in context: 
http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[srinivasa rao lanke]

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: 
http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538p5013540.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[srinivasa rao lanke]

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: 
http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538p5013541.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[srinivasa rao lanke]

 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 -f fit.xtc -s 10nsnvt.tpr -n index.ndx  EOF
2
2
EOF
.
after script 2 grid.cube files imported in VMD
..



[srinivas@cclw1 g_ac-life]$ ./run.sh
 :-)  G  R  O  M  A  C  S  (-:

   Great Red Oystrich Makes All Chemists Sane

:-)  VERSION 4.6.3  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,  
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at  
Uppsala University  The Royal Institute of Technology, Sweden.  
check out http://www.gromacs.org for more information.  

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.  

   :-)  trjconv  (-:

Option Filename  Type Description

  -f10nsnvt.trr  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -o  noPBC.xtc  Output   Trajectory: xtc trr trj gro g96 pdb
  -s10nsnvt.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
pdb
  -n  index.ndx  Input, Opt!  Index file
 -fr frames.ndx  Input, Opt.  Index file
-subcluster.ndx  Input, Opt.  Index file
-drop  drop.xvg  Input, Opt.  xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit  
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel  
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-tu  enum   ps  Time unit: fs, ps, ns, us, ms or s  
-[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-skipint1   Only write every nr-th frame  
-dt  time   0   Only write frame when t MOD dt = first time (ps)
-[no]round   bool   no  Round measurements to nearest picosecond
-dumptime   -1  Dump frame nearest specified time (ps)  
-t0  time   0   Starting time (ps) (default: don't change)  
-timesteptime   0   Change time step between input frames (ps)  
-pbc enum   nonePBC treatment (see help text for full  
description): none, mol, res, atom, nojump,
cluster or whole
-ur  enum   compact  Unit-cell representation: rect, tric or compact
-[no]center  bool   yes Center atoms in box
-boxcenter   enum   tricCenter for -pbc and -center: tric, rect or zero
-box vector 0 0 0   Size for new cubic box (default: read from
input)
-clustercenter vector 0 0 0   Optional starting point for pbc cluster option
-trans   vector 0 0 0   All coordinates will be translated by trans.
This
can advantageously be combined with -pbc mol -ur
compact.
-shift   vector 0 0 0   All coordinates will be shifted by framenr*shift
-fit enum   noneFit molecule to ref structure in the structure  
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive  
-ndecint3   Precision for .xtc and .gro writing in number of
decimal places  
-[no]vel bool   yes Read and 

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

[Christopher Neale]

To help you, I need to see the exact commands that you used. Best is if you can 
put it all in a script, run the script to be sure that you see the problem, and 
then copy and paste the script back to this list. Failing that, copy and paste 
your commands and tell me what your command-line input was to each tool.

Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of srinivasa rao 
lanke srinu1...@hotmail.com
Sent: 26 December 2013 11:12
To: gmx-us...@gromacs.org
Subject: [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 view as an isosurface.

I simulated one molecule with water system
1 step i selected solute i.e molecule and totatel system
2 step also same like 1st step
3 step i selected four atoms from molecule and water OW
grid.cube file created and seen in VMD

I am looking for sdf of molecule group and water Oxygen

I am seeing sdf surface and my molecule atoms are overlapping in 3D view

but most of the publication i have seen that there is a distance between sdf
surface and
water oxygen.

Could you please suggest me how to correct this problem.

thank you very much advance


Srinivas
phd student
IIT hyderabad

--
View this message in context: 
http://gromacs.5086.x6.nabble.com/g-spatial-merging-solvent-ond-solute-need-some-distance-tp5013538.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[srinivasa rao lanke]

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 -f fit.xtc -s 10nsnvt.tpr -n index.ndx  EOF
2
2
EOF
.
after script 2 grid.cube files imported in VMD
..



[srinivas@cclw1 g_ac-life]$ ./run.sh
 :-)  G  R  O  M  A  C  S  (-:

   Great Red Oystrich Makes All Chemists Sane

:-)  VERSION 4.6.3  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,  
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at  
Uppsala University  The Royal Institute of Technology, Sweden.  
check out http://www.gromacs.org for more information.  

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.  

   :-)  trjconv  (-:

Option Filename  Type Description

  -f10nsnvt.trr  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -o  noPBC.xtc  Output   Trajectory: xtc trr trj gro g96 pdb
  -s10nsnvt.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96
pdb
  -n  index.ndx  Input, Opt!  Index file
 -fr frames.ndx  Input, Opt.  Index file
-subcluster.ndx  Input, Opt.  Index file
-drop  drop.xvg  Input, Opt.  xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit  
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel  
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-tu  enum   ps  Time unit: fs, ps, ns, us, ms or s  
-[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-skipint1   Only write every nr-th frame  
-dt  time   0   Only write frame when t MOD dt = first time (ps)
-[no]round   bool   no  Round measurements to nearest picosecond
-dumptime   -1  Dump frame nearest specified time (ps)  
-t0  time   0   Starting time (ps) (default: don't change)  
-timesteptime   0   Change time step between input frames (ps)  
-pbc enum   nonePBC treatment (see help text for full  
description): none, mol, res, atom, nojump,
cluster or whole
-ur  enum   compact  Unit-cell representation: rect, tric or compact
-[no]center  bool   yes Center atoms in box
-boxcenter   enum   tricCenter for -pbc and -center: tric, rect or zero
-box vector 0 0 0   Size for new cubic box (default: read from
input)
-clustercenter vector 0 0 0   Optional starting point for pbc cluster option
-trans   vector 0 0 0   All coordinates will be translated by trans.
This
can advantageously be combined with -pbc mol -ur
compact.
-shift   vector 0 0 0   All coordinates will be shifted by framenr*shift
-fit enum   noneFit molecule to ref structure in the structure  
file: none, rot+trans, rotxy+transxy,
translation, transxy or progressive  
-ndecint3   Precision for .xtc and .gro writing in number of
decimal places  
-[no]vel bool   yes Read and