Re: [gmx-users] RDF calculation from surface of protein

[ISHRAT JAHAN]

-surf flag is used with -ref flag. Provide the reference file in the -ref
flag.

On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash 
wrote:

> Hi all,
>
> I am trying to calculate the RDF between the protein surface and the
> centre of mass of my ligand and water molecules. Please find below the
> command I used:
>
> gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin
> 0.02 -cn number.xvg -surf mol -seltype mol_com
>
>
> I get the following error:
>
>
>
> Inconsistency in user input:
> -surf only works with -ref that consists of atoms
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I am wondering what this error means? My ref group does contain atoms? Any
> guidance will be much appreciated :)
>
>
> Akash
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-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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[gmx-users] RDF calculation from surface of protein

[Pandya, Akash]

Hi all,

I am trying to calculate the RDF between the protein surface and the centre of 
mass of my ligand and water molecules. Please find below the command I used:

gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02 
-cn number.xvg -surf mol -seltype mol_com


I get the following error:



Inconsistency in user input:
-surf only works with -ref that consists of atoms

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am wondering what this error means? My ref group does contain atoms? Any 
guidance will be much appreciated :)


Akash
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Re: [gmx-users] RDF between larger molecules

[Justin Lemkul]

On 1/20/20 10:00 AM, Gmx QA wrote:

Thanks Justin!

Can you also comment on the other issue, the lack of smoothness? I guess
this is because I don't have that many individual coms per bin to
accurately compute the rdf? At least I think that makes sense since when I
increase the value of -bin in gmx rdf I get an increase in "smoothness" and
fewer "jump" back and forth.



It's just sampling. RDF analysis was designed for pure liquids, in which 
there are a huge number of the same type of interaction. You have a 
heterogeneous system, so in the absence of much longer simulations, 
you're not going to get smooth RDFs.


-Justin



Den mån 20 jan. 2020 kl 15:50 skrev Justin Lemkul :



On 1/20/20 9:48 AM, Gmx QA wrote:

Hi list,

I am working on a system that contains lipids, but since there is no

water

present they do not form a typical bilayer.

In these systems I also have some smaller drug-like molecules. What would
be the best way to get a proper rdf-function between the lipids and the
drugs? Since both types of molecules are larger than single atoms, I

tried

to calculate a com-com rdf using

-selrpos whole_mol_com -seltype whole_mol_com

but the resulting curve is very rugged (i.e. not as smooth as
the atom-rdf's typically shown). The minimum distance (the distance
below which the pdf is zero) also appears to be quite small, since one

the

molecules is a lipid I would have expected a larger distance than
the corresponding value seen in e.g. an oxygen-oxygen rdf for water.

Might all of this be consequences of the fact that I have a com-com rdf
between a limited number of molecules?

Yes, likely. You could in principle have a COM-COM RDF value very close
to r=0 if a lipid were to wrap around a drug molecule, so I don't think
any of your results are unexpected.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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==

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] RDF between larger molecules

[Gmx QA]

Thanks Justin!

Can you also comment on the other issue, the lack of smoothness? I guess
this is because I don't have that many individual coms per bin to
accurately compute the rdf? At least I think that makes sense since when I
increase the value of -bin in gmx rdf I get an increase in "smoothness" and
fewer "jump" back and forth.



Den mån 20 jan. 2020 kl 15:50 skrev Justin Lemkul :

>
>
> On 1/20/20 9:48 AM, Gmx QA wrote:
> > Hi list,
> >
> > I am working on a system that contains lipids, but since there is no
> water
> > present they do not form a typical bilayer.
> >
> > In these systems I also have some smaller drug-like molecules. What would
> > be the best way to get a proper rdf-function between the lipids and the
> > drugs? Since both types of molecules are larger than single atoms, I
> tried
> > to calculate a com-com rdf using
> >
> > -selrpos whole_mol_com -seltype whole_mol_com
> >
> > but the resulting curve is very rugged (i.e. not as smooth as
> > the atom-rdf's typically shown). The minimum distance (the distance
> > below which the pdf is zero) also appears to be quite small, since one
> the
> > molecules is a lipid I would have expected a larger distance than
> > the corresponding value seen in e.g. an oxygen-oxygen rdf for water.
> >
> > Might all of this be consequences of the fact that I have a com-com rdf
> > between a limited number of molecules?
>
> Yes, likely. You could in principle have a COM-COM RDF value very close
> to r=0 if a lipid were to wrap around a drug molecule, so I don't think
> any of your results are unexpected.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] RDF between larger molecules

[Justin Lemkul]

On 1/20/20 9:48 AM, Gmx QA wrote:

Hi list,

I am working on a system that contains lipids, but since there is no water
present they do not form a typical bilayer.

In these systems I also have some smaller drug-like molecules. What would
be the best way to get a proper rdf-function between the lipids and the
drugs? Since both types of molecules are larger than single atoms, I tried
to calculate a com-com rdf using

-selrpos whole_mol_com -seltype whole_mol_com

but the resulting curve is very rugged (i.e. not as smooth as
the atom-rdf's typically shown). The minimum distance (the distance
below which the pdf is zero) also appears to be quite small, since one the
molecules is a lipid I would have expected a larger distance than
the corresponding value seen in e.g. an oxygen-oxygen rdf for water.

Might all of this be consequences of the fact that I have a com-com rdf
between a limited number of molecules?


Yes, likely. You could in principle have a COM-COM RDF value very close 
to r=0 if a lipid were to wrap around a drug molecule, so I don't think 
any of your results are unexpected.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] RDF between larger molecules

[Gmx QA]

Hi list,

I am working on a system that contains lipids, but since there is no water
present they do not form a typical bilayer.

In these systems I also have some smaller drug-like molecules. What would
be the best way to get a proper rdf-function between the lipids and the
drugs? Since both types of molecules are larger than single atoms, I tried
to calculate a com-com rdf using

-selrpos whole_mol_com -seltype whole_mol_com

but the resulting curve is very rugged (i.e. not as smooth as
the atom-rdf's typically shown). The minimum distance (the distance
below which the pdf is zero) also appears to be quite small, since one the
molecules is a lipid I would have expected a larger distance than
the corresponding value seen in e.g. an oxygen-oxygen rdf for water.

Might all of this be consequences of the fact that I have a com-com rdf
between a limited number of molecules?

Thanks
/PK
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Re: [gmx-users] rdf

[shakuntala dhurua]

Thank you Justin I will follow
On Sun, 10 Nov 2019, 7:05 pm Justin Lemkul,  wrote:

>
>
> On 11/9/19 11:17 PM, shakuntala dhurua wrote:
> > sir, as i m beginner of gromacs i want to calculate rdf between o-o of
> > only  bulk water simulation, here i have generate xtc file using gmx rdf
> -n
> > index.ndx -s water5.tpr -f water5.trr -o water5.xtc ,after that for rdf
> > calculation i have used gmx rdf -n index.ndx -s  water5.tpr -f water5.xtc
> > -o rdf_water.xvg then
> >   the out put was like that
> > Available static index groups:
> >   Group  0 "System" (2709 atoms)
> >   Group  1 "Water" (2709 atoms)
> >   Group  2 "SOL" (2709 atoms)
> >   Group  3 "OW" (903 atoms)
> > Specify a selection for option 'ref'
> > (Reference selection for RDF computation):
> > (one per line,  for status/groups, 'help' for help)
> > after putting group 3  it shows below
> >
> > Selection '3' parsed
> > Available static index groups:Selection '3' parsed
> > Available static index groups:
> >   Group  0 "System" (2709 atoms)
> >   Group  1 "Water" (2709 atoms)
> >   Group  2 "SOL" (2709 atoms)
> >   Group  3 "OW" (903 atoms)
> > Specify any number of selections for option 'sel'
> > (Selections to compute RDFs for from the reference):
> > (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> >> 3 (here i am selected group 3 again) and it again shows
> > Selection '3' parsed
> > what is this actually i am not able to understand please help me to solve
> > this.
>
> It means the program is reading the group you chose. There's no problem
> here. End your selection with Ctrl+D and the RDF will be computed.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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Re: [gmx-users] rdf

[Justin Lemkul]

On 11/9/19 11:17 PM, shakuntala dhurua wrote:

sir, as i m beginner of gromacs i want to calculate rdf between o-o of
only  bulk water simulation, here i have generate xtc file using gmx rdf -n
index.ndx -s water5.tpr -f water5.trr -o water5.xtc ,after that for rdf
calculation i have used gmx rdf -n index.ndx -s  water5.tpr -f water5.xtc
-o rdf_water.xvg then
  the out put was like that
Available static index groups:
  Group  0 "System" (2709 atoms)
  Group  1 "Water" (2709 atoms)
  Group  2 "SOL" (2709 atoms)
  Group  3 "OW" (903 atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line,  for status/groups, 'help' for help)
after putting group 3  it shows below

Selection '3' parsed
Available static index groups:Selection '3' parsed
Available static index groups:
  Group  0 "System" (2709 atoms)
  Group  1 "Water" (2709 atoms)
  Group  2 "SOL" (2709 atoms)
  Group  3 "OW" (903 atoms)
Specify any number of selections for option 'sel'
(Selections to compute RDFs for from the reference):
(one per line,  for status/groups, 'help' for help, Ctrl-D to end)

3 (here i am selected group 3 again) and it again shows

Selection '3' parsed
what is this actually i am not able to understand please help me to solve
this.


It means the program is reading the group you chose. There's no problem 
here. End your selection with Ctrl+D and the RDF will be computed.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] rdf

[shakuntala dhurua]

sir, as i m beginner of gromacs i want to calculate rdf between o-o of
only  bulk water simulation, here i have generate xtc file using gmx rdf -n
index.ndx -s water5.tpr -f water5.trr -o water5.xtc ,after that for rdf
calculation i have used gmx rdf -n index.ndx -s  water5.tpr -f water5.xtc
-o rdf_water.xvg then
 the out put was like that
Available static index groups:
 Group  0 "System" (2709 atoms)
 Group  1 "Water" (2709 atoms)
 Group  2 "SOL" (2709 atoms)
 Group  3 "OW" (903 atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line,  for status/groups, 'help' for help)
after putting group 3  it shows below

Selection '3' parsed
Available static index groups:Selection '3' parsed
Available static index groups:
 Group  0 "System" (2709 atoms)
 Group  1 "Water" (2709 atoms)
 Group  2 "SOL" (2709 atoms)
 Group  3 "OW" (903 atoms)
Specify any number of selections for option 'sel'
(Selections to compute RDFs for from the reference):
(one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> 3 (here i am selected group 3 again) and it again shows
Selection '3' parsed
what is this actually i am not able to understand please help me to solve
this.



On Sat, Nov 9, 2019 at 7:57 PM Justin Lemkul  wrote:

>
>
> On 11/9/19 1:03 AM, shakuntala dhurua wrote:
> > I am facing proble while calculating rdf , after generating xtc file i
> used
> > flag gmx rdf -s .tpr -f .xtc -n .ndx -o .xvg then from index data i was
> > selected group1 and group2 but there it was written parsed group1 and
> > group2. please suggest me to solve this problem.
>
> Please provide the actual command and relevant screen output, including
> any error message. What you have posted doesn't even sound like an
> error. You chose two groups for a calculation, which were then parsed by
> the rdf program.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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Re: [gmx-users] rdf

[Justin Lemkul]

On 11/9/19 1:03 AM, shakuntala dhurua wrote:

I am facing proble while calculating rdf , after generating xtc file i used
flag gmx rdf -s .tpr -f .xtc -n .ndx -o .xvg then from index data i was
selected group1 and group2 but there it was written parsed group1 and
group2. please suggest me to solve this problem.


Please provide the actual command and relevant screen output, including 
any error message. What you have posted doesn't even sound like an 
error. You chose two groups for a calculation, which were then parsed by 
the rdf program.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] rdf

[shakuntala dhurua]

I am facing proble while calculating rdf , after generating xtc file i used
flag gmx rdf -s .tpr -f .xtc -n .ndx -o .xvg then from index data i was
selected group1 and group2 but there it was written parsed group1 and
group2. please suggest me to solve this problem.
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Re: [gmx-users] RDF in gromacs

[Dallas Warren]

What is the selection syntax you are actually using? Copy and paste, don't
do from memory.

On Wed, 9 Jan. 2019, 8:40 pm daniel madulu shadrack  Hi,
> I am calculating the rdf of my system as follows.
>
> 1. rdf of oxygen atom of my drug and water this is successful (I just made
> an index file and for water i choose eg. 5 & a OW) this worked fine.
>
> 2. I want now to calculate the rdf of oxygen in my drug and oxygen from the
> hydroxyl group of the chitosan, I am getting difficult on how to select
> only oxygen in chitosan or polymer and make an index file, I am getting
> syntax errors, How should I do?
>
> Help.
>
> --
>
>
> *Regards,   *
> Daniel Madulu Shadrack., (M.Sc. Chem).
> PhD Research Scholar
> (Nanomedicine & Comp. Aided Drug Design)
>
>   dmss...@gmail.com
> -
> *FOR GOD LET US DO MUCH, **QUICK AND **WELL*..
>   *St. Gaspar Del Bufalo*
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[gmx-users] RDF in gromacs

[daniel madulu shadrack]

Hi,
I am calculating the rdf of my system as follows.

1. rdf of oxygen atom of my drug and water this is successful (I just made
an index file and for water i choose eg. 5 & a OW) this worked fine.

2. I want now to calculate the rdf of oxygen in my drug and oxygen from the
hydroxyl group of the chitosan, I am getting difficult on how to select
only oxygen in chitosan or polymer and make an index file, I am getting
syntax errors, How should I do?

Help.

-- 


*Regards,   *
Daniel Madulu Shadrack., (M.Sc. Chem).
PhD Research Scholar
(Nanomedicine & Comp. Aided Drug Design)

  dmss...@gmail.com
-
*FOR GOD LET US DO MUCH, **QUICK AND **WELL*..
  *St. Gaspar Del Bufalo*
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[gmx-users] RDF in a droplet

[Alex]

Dear all,
I have a system contains dispersed molecules of A(# 29) and B(# 14) in
water. A droplet is formed by molecule of A and B after 100 ns of MD
simulations where the B is supposed to more or less be like a shell around
A as a core.
I want to know the relative positions of molecules of A and B (or at least
some atoms of them) respect to each other or respect to the center of mass
of the formed droplet if possible. I guess the GMX RDF can do the job, so,
I am using below command; would you please help me improve the rdf or
please let me know what is wrong with the commands

gmx rdf -f md.xtc -s md.tpe -n index.ndx -o rdfB.xvg -b 99000 -selrpos
mol_cog -ref A -sel B

gmx rdf -f md.xtc -s md.tpe -n index.ndx -o rdfA.xvg -b 99000 -selrpos
mol_cog -ref A -sel A

Thank you
Alex
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Re: [gmx-users] rdf coordination number over time (ns)

[Arun Srikanth]

Hi if you have rdf it is easy to calculate the coordination number by
numerical integration

https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions

Arun

On Mon, Nov 26, 2018 at 11:38 AM Maria Luisa  wrote:

> Dear users,
> I need to calculate rdf coordination number over time. I have a pdb
> trajecory of 200 ns, from which I want to evaluate  g(r) and CN of Na-Cl,
> Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number
> in function of time! Can you help me?
>
> Maria Luisa
>
>
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perro...@itm.cnr.it
>
>
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[gmx-users] rdf coordination number over time (ns)

[Maria Luisa]

Dear users,
I need to calculate rdf coordination number over time. I have a pdb
trajecory of 200 ns, from which I want to evaluate  g(r) and CN of Na-Cl,
Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number
in function of time! Can you help me?

Maria Luisa


Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
Italy
email: ml.perro...@itm.cnr.it


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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Thank you for your reply!

Best regards,
Mahsa

On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham 
wrote:

> Hi,
>
> You need a composite selection, eg of an atomtype and residue type or
> molecule type. Make a selection of the atomtype and another of whatever
> seems suitable, and combine them.
>
> Mark
>
> On Sat, Aug 11, 2018, 13:53 Mahsa  wrote:
>
> > Hi Mark,
> >
> > Thank you for your reply!
> >
> > I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> > based on the atom types which worked very well. The only problem is I
> need
> > to also compute the RDF for the O of the side chain with the same atom
> type
> > as the ester O in the polymer. Then with this approach I get both O types
> > in a group while I should have them separately. Could you help me with
> this
> > problem? I don't know how to specify this one for the RDF calculations.
> >
> > Best regards,
> > Mahsa
> >
> >
> >
> >
> >
> > On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > Making a selection with a tool like gmx select or gmx make_ndx is a
> good
> > > way to select e.g. by atomtype.
> > >
> > > Mark
> > >
> > > On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
> > >
> > > > Hello,
> > > >
> > > > I would like to calculate the RDF between some ions and oxygen atoms
> > of a
> > > > polymer. The polymer has ester functional group with two different
> atom
> > > > types O and OS according to GAFF. It has also a side chain with
> > ethereal
> > > > oxygen which has the same atom type as the ester part. How can I
> > specify
> > > > the O of the side chain in the index file to tell it apart from the
> > > other O
> > > > atoms?
> > > > Besides there are around 500 of this atom in the system so changing
> > > > something manually is not a good option either.
> > > >
> > > > Best regards,
> > > > Mahsa
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mark Abraham]

Hi,

You need a composite selection, eg of an atomtype and residue type or
molecule type. Make a selection of the atomtype and another of whatever
seems suitable, and combine them.

Mark

On Sat, Aug 11, 2018, 13:53 Mahsa  wrote:

> Hi Mark,
>
> Thank you for your reply!
>
> I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> based on the atom types which worked very well. The only problem is I need
> to also compute the RDF for the O of the side chain with the same atom type
> as the ester O in the polymer. Then with this approach I get both O types
> in a group while I should have them separately. Could you help me with this
> problem? I don't know how to specify this one for the RDF calculations.
>
> Best regards,
> Mahsa
>
>
>
>
>
> On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Making a selection with a tool like gmx select or gmx make_ndx is a good
> > way to select e.g. by atomtype.
> >
> > Mark
> >
> > On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
> >
> > > Hello,
> > >
> > > I would like to calculate the RDF between some ions and oxygen atoms
> of a
> > > polymer. The polymer has ester functional group with two different atom
> > > types O and OS according to GAFF. It has also a side chain with
> ethereal
> > > oxygen which has the same atom type as the ester part. How can I
> specify
> > > the O of the side chain in the index file to tell it apart from the
> > other O
> > > atoms?
> > > Besides there are around 500 of this atom in the system so changing
> > > something manually is not a good option either.
> > >
> > > Best regards,
> > > Mahsa
> > > --
> > > 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
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Dear Mark,

Could you please comment on my previous question? I would really appreciate
it.

Best regards,
Mahsa

On Sat, Aug 11, 2018 at 12:52 PM, Mahsa  wrote:

> Hi Mark,
>
> Thank you for your reply!
>
> I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> based on the atom types which worked very well. The only problem is I need
> to also compute the RDF for the O of the side chain with the same atom type
> as the ester O in the polymer. Then with this approach I get both O types
> in a group while I should have them separately. Could you help me with this
> problem? I don't know how to specify this one for the RDF calculations.
>
> Best regards,
> Mahsa
>
>
>
>
>
> On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Making a selection with a tool like gmx select or gmx make_ndx is a good
>> way to select e.g. by atomtype.
>>
>> Mark
>>
>> On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
>>
>> > Hello,
>> >
>> > I would like to calculate the RDF between some ions and oxygen atoms of
>> a
>> > polymer. The polymer has ester functional group with two different atom
>> > types O and OS according to GAFF. It has also a side chain with ethereal
>> > oxygen which has the same atom type as the ester part. How can I specify
>> > the O of the side chain in the index file to tell it apart from the
>> other O
>> > atoms?
>> > Besides there are around 500 of this atom in the system so changing
>> > something manually is not a good option either.
>> >
>> > Best regards,
>> > Mahsa
>> > --
>> > 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!
>>
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>>
>
>
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Dallas Warren]

Make the selection based on the atomtype and resname

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Sat, 11 Aug 2018 at 20:53, Mahsa  wrote:
>
> Hi Mark,
>
> Thank you for your reply!
>
> I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> based on the atom types which worked very well. The only problem is I need
> to also compute the RDF for the O of the side chain with the same atom type
> as the ester O in the polymer. Then with this approach I get both O types
> in a group while I should have them separately. Could you help me with this
> problem? I don't know how to specify this one for the RDF calculations.
>
> Best regards,
> Mahsa
>
>
>
>
>
> On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Making a selection with a tool like gmx select or gmx make_ndx is a good
> > way to select e.g. by atomtype.
> >
> > Mark
> >
> > On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
> >
> > > Hello,
> > >
> > > I would like to calculate the RDF between some ions and oxygen atoms of a
> > > polymer. The polymer has ester functional group with two different atom
> > > types O and OS according to GAFF. It has also a side chain with ethereal
> > > oxygen which has the same atom type as the ester part. How can I specify
> > > the O of the side chain in the index file to tell it apart from the
> > other O
> > > atoms?
> > > Besides there are around 500 of this atom in the system so changing
> > > something manually is not a good option either.
> > >
> > > Best regards,
> > > Mahsa
> > > --
> > > 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.
> > >
> > --
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> >
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> >
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Hi Mark,

Thank you for your reply!

I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
based on the atom types which worked very well. The only problem is I need
to also compute the RDF for the O of the side chain with the same atom type
as the ester O in the polymer. Then with this approach I get both O types
in a group while I should have them separately. Could you help me with this
problem? I don't know how to specify this one for the RDF calculations.

Best regards,
Mahsa





On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham 
wrote:

> Hi,
>
> Making a selection with a tool like gmx select or gmx make_ndx is a good
> way to select e.g. by atomtype.
>
> Mark
>
> On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:
>
> > Hello,
> >
> > I would like to calculate the RDF between some ions and oxygen atoms of a
> > polymer. The polymer has ester functional group with two different atom
> > types O and OS according to GAFF. It has also a side chain with ethereal
> > oxygen which has the same atom type as the ester part. How can I specify
> > the O of the side chain in the index file to tell it apart from the
> other O
> > atoms?
> > Besides there are around 500 of this atom in the system so changing
> > something manually is not a good option either.
> >
> > Best regards,
> > Mahsa
> > --
> > 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!
>
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Re: [gmx-users] RDF calculations for certain atoms in a polymer

[Mark Abraham]

Hi,

Making a selection with a tool like gmx select or gmx make_ndx is a good
way to select e.g. by atomtype.

Mark

On Sat, Aug 11, 2018, 12:58 Mahsa  wrote:

> Hello,
>
> I would like to calculate the RDF between some ions and oxygen atoms of a
> polymer. The polymer has ester functional group with two different atom
> types O and OS according to GAFF. It has also a side chain with ethereal
> oxygen which has the same atom type as the ester part. How can I specify
> the O of the side chain in the index file to tell it apart from the other O
> atoms?
> Besides there are around 500 of this atom in the system so changing
> something manually is not a good option either.
>
> Best regards,
> Mahsa
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
> * 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.
>
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[gmx-users] RDF calculations for certain atoms in a polymer

[Mahsa]

Hello,

I would like to calculate the RDF between some ions and oxygen atoms of a
polymer. The polymer has ester functional group with two different atom
types O and OS according to GAFF. It has also a side chain with ethereal
oxygen which has the same atom type as the ester part. How can I specify
the O of the side chain in the index file to tell it apart from the other O
atoms?
Besides there are around 500 of this atom in the system so changing
something manually is not a good option either.

Best regards,
Mahsa
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Re: [gmx-users] rdf at contact

[Faezeh Pousaneh]

I will be grateful if some one can reply my question,


Best regards


On Wed, May 30, 2018 at 4:45 PM, Faezeh Pousaneh 
wrote:

> Hi,
>
> I have a system of similar molecules, I would like to obtain the rdf at
> contact (meaning, at surface of one particle).
> What I try is; I make an index file containing only central atoms of all
> molecules, then I run:
>
>
> gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0
>  -b   14000
>
> ref 0 is a single atom
> ref 1 is rest of atoms
>
>
> Then, I find the rdf value at r=contact (radius of a molecule) from
> rdf.xvg file.
> My problem is I get very different values  for different time intervals
> (after equilibrium) . Why is that so?
>
> I appreciate if sb can help.
> Best regards
>
>
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Re: [gmx-users] rdf at contact

[Dallas Warren]

How noisy is the rdf i.e. what is the bin width, how many atoms etc?
Have you graphed the entire function?  That would be my first
suggestion of the cause.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 31 May 2018 at 00:45, Faezeh Pousaneh  wrote:
> Hi,
>
> I have a system of similar molecules, I would like to obtain the rdf at
> contact (meaning, at surface of one particle).
> What I try is; I make an index file containing only central atoms of all
> molecules, then I run:
>
>
> gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0   -b
>  14000
>
> ref 0 is a single atom
> ref 1 is rest of atoms
>
>
> Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg
> file.
> My problem is I get very different values  for different time intervals
> (after equilibrium) . Why is that so?
>
> I appreciate if sb can help.
> Best regards
> --
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[gmx-users] rdf at contact

[Faezeh Pousaneh]

Hi,

I have a system of similar molecules, I would like to obtain the rdf at
contact (meaning, at surface of one particle).
What I try is; I make an index file containing only central atoms of all
molecules, then I run:


gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0   -b
 14000

ref 0 is a single atom
ref 1 is rest of atoms


Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg
file.
My problem is I get very different values  for different time intervals
(after equilibrium) . Why is that so?

I appreciate if sb can help.
Best regards
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[gmx-users] RDF

[Alex]

Dear all,

I wan to parameterize the interaction between coarse-grained beads of a
molecule and beads of P$ martini water using Votca. So, I want to calculate
the RDF between moecules's beads and water beads in atomistic level as
target RDF.
I know the mapping of the molecule itself so that I know how to calculate
the RDF between molecule's beads in atomistic level easily, but my problem
is with calculation the RDF between molecule's bead and water bead, as I do
not know the mapping of water, so, I wonder if one could help me calculate
the RDF between molecule's beads and water?
Thank you.
Alex
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[gmx-users] RDF calculation

[Esra kaçar]

Dear all,

I have a curved rod-like micelle formed by three different molecules. I
want to calculate the RDF of constituent molecules. I want to select the
center line of the curved cylindir-like structure as a reference point. How
can I do that? I am using Gromacs version 5.1.2. with Martini Force field.
Any suggestions would be helpful.

Many thanks,

Esra
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Re: [gmx-users] RDF brads

[Joe Jordan]

You can just give the selection you would use to make the ndx file directly
to gmx rdf.

You should be fine to average the simulations RDF (and e.g. PCA) are
statistical properties, and averaging should give you better statistics =)

On Wed, Mar 28, 2018 at 11:56 PM, Alex  wrote:

> Dear all,
>
> To obtain the coarse-graine (CG) parameters of a molecule using votca,
> below are the considered beads: (the bead are weighted by atomic weights )
> Bead A contains atoms of " a1, ..., a11"
> Bead B contains atoms of " b1, ..., b9"
> Bead C contains atoms of " c1,..., c13"
>
> Now, to calculate the RDF (A-A, A-B, A-C, B-C, B-B and C-C), in the all
> atom gromacs, would you please confirm me that I have to bundle the atoms
> of a1, ..., a11 in index.ndx (gmx make_ndx) in a section called A (and for
> the rest as well), and then using gmx rdf -ref A -sel B ... I am able to
> calculate a RDF similar to what I get in CG?
>
> One more question:
>
> Since the molecule which I was talking about in the last question is a log
> polymer which is hard to move and also I considered to have 300 molecules
> of that in my all atom MD system, so, I did not simulate my system for a
> long time (25 ns), but rather I simulated the system in multiple short MD
> simulation (5 * 5 ns), each with different initial conf.gro (but all
> include 300 molecules), now, I was wondering how can I calculate the
> physical quantities of the system out of those simulation? for example for
> the RDF, can I average the RDF of the 5 short simulations to get the final
> RDF?
>
> Thank you.
> Best regards,
> Alex
> --
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>



-- 
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[gmx-users] RDF brads

[Alex]

Dear all,

To obtain the coarse-graine (CG) parameters of a molecule using votca,
below are the considered beads: (the bead are weighted by atomic weights )
Bead A contains atoms of " a1, ..., a11"
Bead B contains atoms of " b1, ..., b9"
Bead C contains atoms of " c1,..., c13"

Now, to calculate the RDF (A-A, A-B, A-C, B-C, B-B and C-C), in the all
atom gromacs, would you please confirm me that I have to bundle the atoms
of a1, ..., a11 in index.ndx (gmx make_ndx) in a section called A (and for
the rest as well), and then using gmx rdf -ref A -sel B ... I am able to
calculate a RDF similar to what I get in CG?

One more question:

Since the molecule which I was talking about in the last question is a log
polymer which is hard to move and also I considered to have 300 molecules
of that in my all atom MD system, so, I did not simulate my system for a
long time (25 ns), but rather I simulated the system in multiple short MD
simulation (5 * 5 ns), each with different initial conf.gro (but all
include 300 molecules), now, I was wondering how can I calculate the
physical quantities of the system out of those simulation? for example for
the RDF, can I average the RDF of the 5 short simulations to get the final
RDF?

Thank you.
Best regards,
Alex
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Re: [gmx-users] rdf calculation for wormlike micelles

[Esra kaçar]

Dear Joe,

Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line has a
curved structure and I couldn’t figure out how to select that line as a
reference point. I guess a picture would be more helpful to explain my
purpose. It is similar to the Figure 3 in the paper that I gave the link
below:

https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176

Many thanks,

Esra


2018-03-14 17:51 GMT+03:00 :

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>1. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Esra ka?ar)
>2. Re: gromacs.org_gmx-users Digest, Vol 167, Issue 73 (Joe Jordan)
>3. Umbrella Sampling - good histogram but no result in   profile
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>4. Re: Umbrella Sampling - good histogram but no result in
>   profile (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Wed, 14 Mar 2018 16:28:19 +0300
> From: Esra ka?ar 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue
> 73
> Message-ID:
> 

Re: [gmx-users] rdf calculation for wormlike micelles

[Joe Jordan]

You cannot use a line as the reference. From a brief glance at the paper
you link it seems like maybe you actually want to compute the expectation
value of the micelle backbone, a method known as principle curves which is
a generalization of principle component analysis. At any rate, you should
probably just follow whatever procedure they use in the paper you are
citing.

On Thu, Mar 15, 2018 at 7:48 AM, Esra Kaçar  wrote:

> Dear Joe,
>
> Sorry for the confusion. I am working with martini force field and I have
> three different molecules in the micelle structure. I want to analyze the
> RDF of the constituent molecules with respect to the line that pass through
> the center along with its length. As I mention before this line has a
> curved structure and I couldn’t figure out how to select that line as a
> reference point. I guess a picture would be more helpful to explain my
> purpose. It is similar to the Figure 3 in the paper that I gave the link
> below:
>
> https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176
>
> Many thanks,
>
> Esra
> --
> Gromacs Users mailing list
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Re: [gmx-users] rdf calculation for wormlike micelles

[Esra Kaçar]

Dear Joe,

Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line has a
curved structure and I couldn’t figure out how to select that line as a
reference point. I guess a picture would be more helpful to explain my
purpose. It is similar to the Figure 3 in the paper that I gave the link
below:

https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01176

Many thanks,

Esra
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Re: [gmx-users] rdf calculation for wormlike micelles

[Joe Jordan]

See here for info on the selection syntax
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

On Wed, Mar 14, 2018 at 10:01 AM, Esra Kaçar  wrote:

> Dear all,
>
> I am working on a wormlike micelle that has a curved structure. I want to
> calculate the radial distribution functions of constituent molecules with
> respect to the backbone (the line following the micelle length and
> represents the center of the curved cylindrical structure) of the wormlike
> micelle. Since the structure is curved, I couldn’t find out how to select
> the backbone as a reference point in g_rdf. I am using Gromacs v 5.1.  Any
> suggestions would be appreciated.
>
> Thanks,
>
> Esra
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[gmx-users] rdf calculation for wormlike micelles

[Esra Kaçar]

Dear all,

I am working on a wormlike micelle that has a curved structure. I want to
calculate the radial distribution functions of constituent molecules with
respect to the backbone (the line following the micelle length and
represents the center of the curved cylindrical structure) of the wormlike
micelle. Since the structure is curved, I couldn’t find out how to select
the backbone as a reference point in g_rdf. I am using Gromacs v 5.1.  Any
suggestions would be appreciated.

Thanks,

Esra
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Re: [gmx-users] RDF from NPT simulation?

[Justin Lemkul]

On 11/2/17 7:28 AM, Sudip Das wrote:

Dear Justin,

Should I have to use any flag(s) with 'rdf' module to scale the coordinates
for fixing the box size? I didn't find such flag in 'rdf' module.


There are no special flags. GROMACS commands deal with box vectors 
intrinsically.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] RDF from NPT simulation?

[Sudip Das]

Dear Justin,

Should I have to use any flag(s) with 'rdf' module to scale the coordinates
for fixing the box size? I didn't find such flag in 'rdf' module.

Please help.

Regards,
Sudip

On Thu, Nov 2, 2017 at 4:41 PM, Justin Lemkul  wrote:

>
>
> On 11/2/17 6:39 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT
>> simulation trajectory (where box size changes from frame to frame)?
>>
> Yes.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] RDF from NPT simulation?

[Justin Lemkul]

On 11/2/17 6:39 AM, Sudip Das wrote:

Dear All,

Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT
simulation trajectory (where box size changes from frame to frame)?

Yes.

-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] RDF from NPT simulation?

[Sudip Das]

Dear All,

Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT
simulation trajectory (where box size changes from frame to frame)?

Thanks in advance.

Regards,
Sudip
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Re: [gmx-users] RDF

[Dallas Warren]

No idea what a surface distribution function is, and how it is
generated.  But I suspect that those two are not the same.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 23 August 2017 at 14:27, RAHUL SURESH  wrote:
> Thank you Sir,
>
> Is spatial distribution function is same as that of surface distribution
> function?
>
> On Wed, Aug 23, 2017 at 9:39 AM, Dallas Warren 
> wrote:
>
>> https://www.google.com.au/search?q=gromacs+sdf
>>
>> i.e. gmx spatial
>>
>> Unfortunately, it only currently will work for a single reference
>> molecule.  There use to be a g_sdf that would work for multiple copies
>> of the reference, much in the same manner that gmx rdf does.  So if
>> that is what you are after, you will need to install that older
>> version and use that to generate it.
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.war...@monash.edu
>> -
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>>
>> On 23 August 2017 at 13:27, RAHUL SURESH  wrote:
>> > Dear Warren,
>> >
>> > Thanks a lot. How will I be able to calculate SDF using Gromacs..?
>> >
>> >
>> >
>> > On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren 
>> > wrote:
>> >
>> >> SDF (Spatial Distribution Function) is simply a three dimensional RDF.
>> >> So instead of simply having a probability associated with each radius
>> >> (r), it provides a probability associated with each (x,y,z) point.
>> >>
>> >> VMD can display the SDF generated by GROMACS.
>> >> Catch ya,
>> >>
>> >> Dr. Dallas Warren
>> >> Drug Delivery, Disposition and Dynamics
>> >> Monash Institute of Pharmaceutical Sciences, Monash University
>> >> 381 Royal Parade, Parkville VIC 3052
>> >> dallas.war...@monash.edu
>> >> -
>> >> When the only tool you own is a hammer, every problem begins to
>> resemble a
>> >> nail.
>> >>
>> >>
>> >> On 18 August 2017 at 21:47, RAHUL SURESH 
>> wrote:
>> >> > Hi Dan
>> >> >
>> >> > Thank you so much for you descriptive answers. I have few
>> clarifications
>> >> > that I have posted here. I will go through the papers here.
>> >> >
>> >> > On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil 
>> wrote:
>> >> >
>> >> >> Hi Rahul,
>> >> >>
>> >> >> I can't find the exact papers right now, but I remember seeing some
>> >> >> inconsistency in how people name these functions especially the
>> radial
>> >> >> distribution function and pair correlation functions.
>> >> >>
>> >> >> If we go far back into literature, we can see JG Kirkwood using pair
>> >> >> correlation functions as functions of both the distance and the
>> relative
>> >> >> orientation between the pairs [The Journal of Chemical Physics 19,
>> 774
>> >> >> (1951); doi: 10.1063/1.1748352]. I don't know if he is the
>> "inventor" of
>> >> >> the RDF, but he was one of the earliest to use it extensively in
>> >> theories.
>> >> >> When you average the pair correlation functions over the relative
>> >> >> orientations, you get the radial distribution function which is a
>> >> function
>> >> >> of distance only.
>> >> >
>> >> >
>> >> > That was very informative. But as now it can be calculated as a whole
>> >> > easily using various tools.
>> >> >
>> >> >
>> >> >> I think I've seen newer papers use RDF/PCF/PDF somewhat
>> >> >> interchangeably although I can't find these right now... Most people
>> >> mean
>> >> >> the RDF but you can always look at the data to know what they mean.
>> >> >>
>> >> >
>> >> > I have come across people describing RDF analysis between water and
>> water
>> >> > and I always wonder what does it means. RDF can be done between
>> protein
>> >> and
>> >> > water to know the distribution of water around protein with default
>> >> center
>> >> > of mass(My little knowledge) and what co-ordination number contribute
>> to
>> >> > RDF has always been a puzzle for me.
>> >> >
>> >> >>
>> >> >> I never used surface distribution functions, hopefully someone else
>> can
>> >> >> bring you up to date on that one (How is the surface defined?).
>> >> >>
>> >> >
>> >> > I will be happy if some one can explain SDF and any particular tool to
>> >> > analyze it.
>> >> >
>> >> >>
>> >> >> But there is also the spatial distribution functions, which now a
>> >> function
>> >> >> in 3D spherical coordinates. It gives the average density of
>> particles
>> >> at
>> >> >> given (r, theta, phi). In this paper they normalize it by the bulk
>> >> density,
>> >> 

Re: [gmx-users] RDF

[RAHUL SURESH]

Thank you Sir,

Is spatial distribution function is same as that of surface distribution
function?

On Wed, Aug 23, 2017 at 9:39 AM, Dallas Warren 
wrote:

> https://www.google.com.au/search?q=gromacs+sdf
>
> i.e. gmx spatial
>
> Unfortunately, it only currently will work for a single reference
> molecule.  There use to be a g_sdf that would work for multiple copies
> of the reference, much in the same manner that gmx rdf does.  So if
> that is what you are after, you will need to install that older
> version and use that to generate it.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 23 August 2017 at 13:27, RAHUL SURESH  wrote:
> > Dear Warren,
> >
> > Thanks a lot. How will I be able to calculate SDF using Gromacs..?
> >
> >
> >
> > On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren 
> > wrote:
> >
> >> SDF (Spatial Distribution Function) is simply a three dimensional RDF.
> >> So instead of simply having a probability associated with each radius
> >> (r), it provides a probability associated with each (x,y,z) point.
> >>
> >> VMD can display the SDF generated by GROMACS.
> >> Catch ya,
> >>
> >> Dr. Dallas Warren
> >> Drug Delivery, Disposition and Dynamics
> >> Monash Institute of Pharmaceutical Sciences, Monash University
> >> 381 Royal Parade, Parkville VIC 3052
> >> dallas.war...@monash.edu
> >> -
> >> When the only tool you own is a hammer, every problem begins to
> resemble a
> >> nail.
> >>
> >>
> >> On 18 August 2017 at 21:47, RAHUL SURESH 
> wrote:
> >> > Hi Dan
> >> >
> >> > Thank you so much for you descriptive answers. I have few
> clarifications
> >> > that I have posted here. I will go through the papers here.
> >> >
> >> > On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil 
> wrote:
> >> >
> >> >> Hi Rahul,
> >> >>
> >> >> I can't find the exact papers right now, but I remember seeing some
> >> >> inconsistency in how people name these functions especially the
> radial
> >> >> distribution function and pair correlation functions.
> >> >>
> >> >> If we go far back into literature, we can see JG Kirkwood using pair
> >> >> correlation functions as functions of both the distance and the
> relative
> >> >> orientation between the pairs [The Journal of Chemical Physics 19,
> 774
> >> >> (1951); doi: 10.1063/1.1748352]. I don't know if he is the
> "inventor" of
> >> >> the RDF, but he was one of the earliest to use it extensively in
> >> theories.
> >> >> When you average the pair correlation functions over the relative
> >> >> orientations, you get the radial distribution function which is a
> >> function
> >> >> of distance only.
> >> >
> >> >
> >> > That was very informative. But as now it can be calculated as a whole
> >> > easily using various tools.
> >> >
> >> >
> >> >> I think I've seen newer papers use RDF/PCF/PDF somewhat
> >> >> interchangeably although I can't find these right now... Most people
> >> mean
> >> >> the RDF but you can always look at the data to know what they mean.
> >> >>
> >> >
> >> > I have come across people describing RDF analysis between water and
> water
> >> > and I always wonder what does it means. RDF can be done between
> protein
> >> and
> >> > water to know the distribution of water around protein with default
> >> center
> >> > of mass(My little knowledge) and what co-ordination number contribute
> to
> >> > RDF has always been a puzzle for me.
> >> >
> >> >>
> >> >> I never used surface distribution functions, hopefully someone else
> can
> >> >> bring you up to date on that one (How is the surface defined?).
> >> >>
> >> >
> >> > I will be happy if some one can explain SDF and any particular tool to
> >> > analyze it.
> >> >
> >> >>
> >> >> But there is also the spatial distribution functions, which now a
> >> function
> >> >> in 3D spherical coordinates. It gives the average density of
> particles
> >> at
> >> >> given (r, theta, phi). In this paper they normalize it by the bulk
> >> density,
> >> >> I am not sure if everyone does the same. (doi: 10.1063/1.465158)
> >> >>
> >> >
> >> > Thank you. I guess it can be calculated using gmx spatial
> >> >
> >> >>
> >> >> I think "radial pair distribution function" is synonymous with the
> RDF
> >> like
> >> >> you said.
> >> >>
> >> >
> >> > Yeah VMD use it as Radial pair distribution function.
> >> >
> >> >>
> >> >> Partial radial distribution function is for multicomponent systems.
> In a
> >> >> single component system, there is only one RDF and that is the total
> >> RDF.
> >> >> In a two component system,
> >> >
> >> >
> >> > what do you mean by  two component system?
> >> >
> 

Re: [gmx-users] RDF

[Dallas Warren]

https://www.google.com.au/search?q=gromacs+sdf

i.e. gmx spatial

Unfortunately, it only currently will work for a single reference
molecule.  There use to be a g_sdf that would work for multiple copies
of the reference, much in the same manner that gmx rdf does.  So if
that is what you are after, you will need to install that older
version and use that to generate it.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 23 August 2017 at 13:27, RAHUL SURESH  wrote:
> Dear Warren,
>
> Thanks a lot. How will I be able to calculate SDF using Gromacs..?
>
>
>
> On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren 
> wrote:
>
>> SDF (Spatial Distribution Function) is simply a three dimensional RDF.
>> So instead of simply having a probability associated with each radius
>> (r), it provides a probability associated with each (x,y,z) point.
>>
>> VMD can display the SDF generated by GROMACS.
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.war...@monash.edu
>> -
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>>
>> On 18 August 2017 at 21:47, RAHUL SURESH  wrote:
>> > Hi Dan
>> >
>> > Thank you so much for you descriptive answers. I have few clarifications
>> > that I have posted here. I will go through the papers here.
>> >
>> > On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil  wrote:
>> >
>> >> Hi Rahul,
>> >>
>> >> I can't find the exact papers right now, but I remember seeing some
>> >> inconsistency in how people name these functions especially the radial
>> >> distribution function and pair correlation functions.
>> >>
>> >> If we go far back into literature, we can see JG Kirkwood using pair
>> >> correlation functions as functions of both the distance and the relative
>> >> orientation between the pairs [The Journal of Chemical Physics 19, 774
>> >> (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
>> >> the RDF, but he was one of the earliest to use it extensively in
>> theories.
>> >> When you average the pair correlation functions over the relative
>> >> orientations, you get the radial distribution function which is a
>> function
>> >> of distance only.
>> >
>> >
>> > That was very informative. But as now it can be calculated as a whole
>> > easily using various tools.
>> >
>> >
>> >> I think I've seen newer papers use RDF/PCF/PDF somewhat
>> >> interchangeably although I can't find these right now... Most people
>> mean
>> >> the RDF but you can always look at the data to know what they mean.
>> >>
>> >
>> > I have come across people describing RDF analysis between water and water
>> > and I always wonder what does it means. RDF can be done between protein
>> and
>> > water to know the distribution of water around protein with default
>> center
>> > of mass(My little knowledge) and what co-ordination number contribute to
>> > RDF has always been a puzzle for me.
>> >
>> >>
>> >> I never used surface distribution functions, hopefully someone else can
>> >> bring you up to date on that one (How is the surface defined?).
>> >>
>> >
>> > I will be happy if some one can explain SDF and any particular tool to
>> > analyze it.
>> >
>> >>
>> >> But there is also the spatial distribution functions, which now a
>> function
>> >> in 3D spherical coordinates. It gives the average density of particles
>> at
>> >> given (r, theta, phi). In this paper they normalize it by the bulk
>> density,
>> >> I am not sure if everyone does the same. (doi: 10.1063/1.465158)
>> >>
>> >
>> > Thank you. I guess it can be calculated using gmx spatial
>> >
>> >>
>> >> I think "radial pair distribution function" is synonymous with the RDF
>> like
>> >> you said.
>> >>
>> >
>> > Yeah VMD use it as Radial pair distribution function.
>> >
>> >>
>> >> Partial radial distribution function is for multicomponent systems. In a
>> >> single component system, there is only one RDF and that is the total
>> RDF.
>> >> In a two component system,
>> >
>> >
>> > what do you mean by  two component system?
>> >
>> >
>> >> there are 3 (AA, AB, BB) partial radial
>> >> distribution functions.
>> >>
>> >> Hope that helps!
>> >>
>> >> Dan
>> >>
>> >> On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
>> >> wrote:
>> >>
>> >> > Radial Distribution Function, Surface Distribution Function(SDF),
>> Radial
>> >> > Pair Distribution Function and Partial Radial Distribution Function.
>> >> >
>> >> > What makes the difference in all the four?
>> >> >
>> >> > 

Re: [gmx-users] RDF

[RAHUL SURESH]

Dear Warren,

Thanks a lot. How will I be able to calculate SDF using Gromacs..?



On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren 
wrote:

> SDF (Spatial Distribution Function) is simply a three dimensional RDF.
> So instead of simply having a probability associated with each radius
> (r), it provides a probability associated with each (x,y,z) point.
>
> VMD can display the SDF generated by GROMACS.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 18 August 2017 at 21:47, RAHUL SURESH  wrote:
> > Hi Dan
> >
> > Thank you so much for you descriptive answers. I have few clarifications
> > that I have posted here. I will go through the papers here.
> >
> > On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil  wrote:
> >
> >> Hi Rahul,
> >>
> >> I can't find the exact papers right now, but I remember seeing some
> >> inconsistency in how people name these functions especially the radial
> >> distribution function and pair correlation functions.
> >>
> >> If we go far back into literature, we can see JG Kirkwood using pair
> >> correlation functions as functions of both the distance and the relative
> >> orientation between the pairs [The Journal of Chemical Physics 19, 774
> >> (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
> >> the RDF, but he was one of the earliest to use it extensively in
> theories.
> >> When you average the pair correlation functions over the relative
> >> orientations, you get the radial distribution function which is a
> function
> >> of distance only.
> >
> >
> > That was very informative. But as now it can be calculated as a whole
> > easily using various tools.
> >
> >
> >> I think I've seen newer papers use RDF/PCF/PDF somewhat
> >> interchangeably although I can't find these right now... Most people
> mean
> >> the RDF but you can always look at the data to know what they mean.
> >>
> >
> > I have come across people describing RDF analysis between water and water
> > and I always wonder what does it means. RDF can be done between protein
> and
> > water to know the distribution of water around protein with default
> center
> > of mass(My little knowledge) and what co-ordination number contribute to
> > RDF has always been a puzzle for me.
> >
> >>
> >> I never used surface distribution functions, hopefully someone else can
> >> bring you up to date on that one (How is the surface defined?).
> >>
> >
> > I will be happy if some one can explain SDF and any particular tool to
> > analyze it.
> >
> >>
> >> But there is also the spatial distribution functions, which now a
> function
> >> in 3D spherical coordinates. It gives the average density of particles
> at
> >> given (r, theta, phi). In this paper they normalize it by the bulk
> density,
> >> I am not sure if everyone does the same. (doi: 10.1063/1.465158)
> >>
> >
> > Thank you. I guess it can be calculated using gmx spatial
> >
> >>
> >> I think "radial pair distribution function" is synonymous with the RDF
> like
> >> you said.
> >>
> >
> > Yeah VMD use it as Radial pair distribution function.
> >
> >>
> >> Partial radial distribution function is for multicomponent systems. In a
> >> single component system, there is only one RDF and that is the total
> RDF.
> >> In a two component system,
> >
> >
> > what do you mean by  two component system?
> >
> >
> >> there are 3 (AA, AB, BB) partial radial
> >> distribution functions.
> >>
> >> Hope that helps!
> >>
> >> Dan
> >>
> >> On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
> >> wrote:
> >>
> >> > Radial Distribution Function, Surface Distribution Function(SDF),
> Radial
> >> > Pair Distribution Function and Partial Radial Distribution Function.
> >> >
> >> > What makes the difference in all the four?
> >> >
> >> > Have gone through lot pages and literature. Somehow one or the other
> >> piece
> >> > of explanation confuses me.
> >> >
> >> > Can I have a short explanation of all?
> >> >
> >> > RDF and R-pair DF one and the same?
> >> >
> >> > How do I calculate SDF and Partial-RDF if it is different from others?
> >> >
> >> > --
> >> > *Regards,*
> >> > *Rahul Suresh*
> >> > *Research Scholar*
> >> > *Bharathiar University*
> >> > *Coimbatore*
> >> > --
> >> > 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] RDF

[Dallas Warren]

SDF (Spatial Distribution Function) is simply a three dimensional RDF.
So instead of simply having a probability associated with each radius
(r), it provides a probability associated with each (x,y,z) point.

VMD can display the SDF generated by GROMACS.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 18 August 2017 at 21:47, RAHUL SURESH  wrote:
> Hi Dan
>
> Thank you so much for you descriptive answers. I have few clarifications
> that I have posted here. I will go through the papers here.
>
> On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil  wrote:
>
>> Hi Rahul,
>>
>> I can't find the exact papers right now, but I remember seeing some
>> inconsistency in how people name these functions especially the radial
>> distribution function and pair correlation functions.
>>
>> If we go far back into literature, we can see JG Kirkwood using pair
>> correlation functions as functions of both the distance and the relative
>> orientation between the pairs [The Journal of Chemical Physics 19, 774
>> (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
>> the RDF, but he was one of the earliest to use it extensively in theories.
>> When you average the pair correlation functions over the relative
>> orientations, you get the radial distribution function which is a function
>> of distance only.
>
>
> That was very informative. But as now it can be calculated as a whole
> easily using various tools.
>
>
>> I think I've seen newer papers use RDF/PCF/PDF somewhat
>> interchangeably although I can't find these right now... Most people mean
>> the RDF but you can always look at the data to know what they mean.
>>
>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>
>>
>> I never used surface distribution functions, hopefully someone else can
>> bring you up to date on that one (How is the surface defined?).
>>
>
> I will be happy if some one can explain SDF and any particular tool to
> analyze it.
>
>>
>> But there is also the spatial distribution functions, which now a function
>> in 3D spherical coordinates. It gives the average density of particles at
>> given (r, theta, phi). In this paper they normalize it by the bulk density,
>> I am not sure if everyone does the same. (doi: 10.1063/1.465158)
>>
>
> Thank you. I guess it can be calculated using gmx spatial
>
>>
>> I think "radial pair distribution function" is synonymous with the RDF like
>> you said.
>>
>
> Yeah VMD use it as Radial pair distribution function.
>
>>
>> Partial radial distribution function is for multicomponent systems. In a
>> single component system, there is only one RDF and that is the total RDF.
>> In a two component system,
>
>
> what do you mean by  two component system?
>
>
>> there are 3 (AA, AB, BB) partial radial
>> distribution functions.
>>
>> Hope that helps!
>>
>> Dan
>>
>> On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
>> wrote:
>>
>> > Radial Distribution Function, Surface Distribution Function(SDF), Radial
>> > Pair Distribution Function and Partial Radial Distribution Function.
>> >
>> > What makes the difference in all the four?
>> >
>> > Have gone through lot pages and literature. Somehow one or the other
>> piece
>> > of explanation confuses me.
>> >
>> > Can I have a short explanation of all?
>> >
>> > RDF and R-pair DF one and the same?
>> >
>> > How do I calculate SDF and Partial-RDF if it is different from others?
>> >
>> > --
>> > *Regards,*
>> > *Rahul Suresh*
>> > *Research Scholar*
>> > *Bharathiar University*
>> > *Coimbatore*
>> > --
>> > 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.
>>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> 

Re: [gmx-users] RDF

[Dan Gil]

>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>

what do you mean by  two component system?
>

These questions be answered together at once. Imagine that a protein is
dissolved in water and urea solution. This system has 3 components (water,
urea, and protein). So there can be 6 RDFs: g_ww, g_uu, g_pp, g_wu, g_wp,
g_up. "w" means water, "u" means urea, "p" means protein (If there is only
one protein molecule, than g_pp should be zero).

Like you said, we can study the distribution of water around proteins. You
can also use RDFs far more things than just protein systems. It can be used
for salts in water, mixtures of organic solvents, etc.

Coordination number is related to the radial distribution function. This
Wikipedia page (https://en.wikipedia.org/wiki/Coordination_number) has a
one method of calculating the coordination number from RDFs. For example,
in a protein + water + urea system, you may be able to find the number of
water molecules and the number of urea molecules around the protein in each
solvation shell. These numbers are averages over time, not the actual
number at a moment in time. I think this method of calculating CN might be
a quick and easy way to see if its worth using better methods (e.g.
deconvoluting each solvation shell before integration). If your protein is
very large, I can imagine this being a more difficult problem, but I don't
know for sure.

On Fri, Aug 18, 2017 at 7:47 AM, RAHUL SURESH 
wrote:

> Hi Dan
>
> Thank you so much for you descriptive answers. I have few clarifications
> that I have posted here. I will go through the papers here.
>
> On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil  wrote:
>
> > Hi Rahul,
> >
> > I can't find the exact papers right now, but I remember seeing some
> > inconsistency in how people name these functions especially the radial
> > distribution function and pair correlation functions.
> >
> > If we go far back into literature, we can see JG Kirkwood using pair
> > correlation functions as functions of both the distance and the relative
> > orientation between the pairs [The Journal of Chemical Physics 19, 774
> > (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
> > the RDF, but he was one of the earliest to use it extensively in
> theories.
> > When you average the pair correlation functions over the relative
> > orientations, you get the radial distribution function which is a
> function
> > of distance only.
>
>
> That was very informative. But as now it can be calculated as a whole
> easily using various tools.
>
>
> > I think I've seen newer papers use RDF/PCF/PDF somewhat
> > interchangeably although I can't find these right now... Most people mean
> > the RDF but you can always look at the data to know what they mean.
> >
>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>
> >
> > I never used surface distribution functions, hopefully someone else can
> > bring you up to date on that one (How is the surface defined?).
> >
>
> I will be happy if some one can explain SDF and any particular tool to
> analyze it.
>
> >
> > But there is also the spatial distribution functions, which now a
> function
> > in 3D spherical coordinates. It gives the average density of particles at
> > given (r, theta, phi). In this paper they normalize it by the bulk
> density,
> > I am not sure if everyone does the same. (doi: 10.1063/1.465158)
> >
>
> Thank you. I guess it can be calculated using gmx spatial
>
> >
> > I think "radial pair distribution function" is synonymous with the RDF
> like
> > you said.
> >
>
> Yeah VMD use it as Radial pair distribution function.
>
> >
> > Partial radial distribution function is for multicomponent systems. In a
> > single component system, there is only one RDF and that is the total RDF.
> > In a two component system,
>
>
> what do you mean by  two component system?
>
>
> > there are 3 (AA, AB, BB) partial radial
> > distribution functions.
> >
> > Hope that helps!
> >
> > Dan
> >
> > On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
> > wrote:
> >
> > > Radial Distribution Function, Surface Distribution Function(SDF),
> Radial
> > > Pair Distribution Function and Partial Radial Distribution Function.
> > >
> > > What makes the difference in all the four?
> > >
> > > Have gone through lot pages and literature. Somehow one or the other
> > piece

Re: [gmx-users] RDF

[RAHUL SURESH]

Hi Dan

Thank you so much for you descriptive answers. I have few clarifications
that I have posted here. I will go through the papers here.

On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil  wrote:

> Hi Rahul,
>
> I can't find the exact papers right now, but I remember seeing some
> inconsistency in how people name these functions especially the radial
> distribution function and pair correlation functions.
>
> If we go far back into literature, we can see JG Kirkwood using pair
> correlation functions as functions of both the distance and the relative
> orientation between the pairs [The Journal of Chemical Physics 19, 774
> (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
> the RDF, but he was one of the earliest to use it extensively in theories.
> When you average the pair correlation functions over the relative
> orientations, you get the radial distribution function which is a function
> of distance only.


That was very informative. But as now it can be calculated as a whole
easily using various tools.


> I think I've seen newer papers use RDF/PCF/PDF somewhat
> interchangeably although I can't find these right now... Most people mean
> the RDF but you can always look at the data to know what they mean.
>

I have come across people describing RDF analysis between water and water
and I always wonder what does it means. RDF can be done between protein and
water to know the distribution of water around protein with default center
of mass(My little knowledge) and what co-ordination number contribute to
RDF has always been a puzzle for me.

>
> I never used surface distribution functions, hopefully someone else can
> bring you up to date on that one (How is the surface defined?).
>

I will be happy if some one can explain SDF and any particular tool to
analyze it.

>
> But there is also the spatial distribution functions, which now a function
> in 3D spherical coordinates. It gives the average density of particles at
> given (r, theta, phi). In this paper they normalize it by the bulk density,
> I am not sure if everyone does the same. (doi: 10.1063/1.465158)
>

Thank you. I guess it can be calculated using gmx spatial

>
> I think "radial pair distribution function" is synonymous with the RDF like
> you said.
>

Yeah VMD use it as Radial pair distribution function.

>
> Partial radial distribution function is for multicomponent systems. In a
> single component system, there is only one RDF and that is the total RDF.
> In a two component system,


what do you mean by  two component system?


> there are 3 (AA, AB, BB) partial radial
> distribution functions.
>
> Hope that helps!
>
> Dan
>
> On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
> wrote:
>
> > Radial Distribution Function, Surface Distribution Function(SDF), Radial
> > Pair Distribution Function and Partial Radial Distribution Function.
> >
> > What makes the difference in all the four?
> >
> > Have gone through lot pages and literature. Somehow one or the other
> piece
> > of explanation confuses me.
> >
> > Can I have a short explanation of all?
> >
> > RDF and R-pair DF one and the same?
> >
> > How do I calculate SDF and Partial-RDF if it is different from others?
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > 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!
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] RDF

[Dan Gil]

Hi Rahul,

I can't find the exact papers right now, but I remember seeing some
inconsistency in how people name these functions especially the radial
distribution function and pair correlation functions.

If we go far back into literature, we can see JG Kirkwood using pair
correlation functions as functions of both the distance and the relative
orientation between the pairs [The Journal of Chemical Physics 19, 774
(1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
the RDF, but he was one of the earliest to use it extensively in theories.
When you average the pair correlation functions over the relative
orientations, you get the radial distribution function which is a function
of distance only. I think I've seen newer papers use RDF/PCF/PDF somewhat
interchangeably although I can't find these right now... Most people mean
the RDF but you can always look at the data to know what they mean.

I never used surface distribution functions, hopefully someone else can
bring you up to date on that one (How is the surface defined?).

But there is also the spatial distribution functions, which now a function
in 3D spherical coordinates. It gives the average density of particles at
given (r, theta, phi). In this paper they normalize it by the bulk density,
I am not sure if everyone does the same. (doi: 10.1063/1.465158)

I think "radial pair distribution function" is synonymous with the RDF like
you said.

Partial radial distribution function is for multicomponent systems. In a
single component system, there is only one RDF and that is the total RDF.
In a two component system, there are 3 (AA, AB, BB) partial radial
distribution functions.

Hope that helps!

Dan

On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
wrote:

> Radial Distribution Function, Surface Distribution Function(SDF), Radial
> Pair Distribution Function and Partial Radial Distribution Function.
>
> What makes the difference in all the four?
>
> Have gone through lot pages and literature. Somehow one or the other piece
> of explanation confuses me.
>
> Can I have a short explanation of all?
>
> RDF and R-pair DF one and the same?
>
> How do I calculate SDF and Partial-RDF if it is different from others?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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.
>
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Re: [gmx-users] RDF Values

[spss4]

 I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5
nm.- Message from "Pandya, Akash" <akash.pandya...@ucl.ac.uk> -
    Date: Mon, 31 Jul 2017 07:29:19 +
    From: "Pandya, Akash" <akash.pandya...@ucl.ac.uk>
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] RDF Values
      To: gmx-us...@gromacs.org


Hi all,

I am calculating the RDF from a particular residue to a particular
glycine molecule. I created an index file for both to do this. My
simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm.
I have viewed my trajectory and all the components stay inside the box.
Please could someone tell me how to overcome this issue? My command line
is below:

gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 6
-ref -sel -bin 0.5 -norm rdf

Akash
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- End message from "Pandya, Akash" <akash.pandya...@ucl.ac.uk> -
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Re: [gmx-users] RDF Values

[saima kalsoom]

hi dear!can anyone please suggest me what does it mean."In chosen Force field 
there is no residue type for QLN"there was no QLN in our origin file. There is 
always a problem when i select any force field.regards 

On Monday, 31 July 2017, 12:29, "Pandya, Akash"  
wrote:
 

 Hi all,

I am calculating the RDF from a particular residue to a particular glycine 
molecule. I created an index file for both to do this. My simulation box is 
1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my 
trajectory and all the components stay inside the box. Please could someone 
tell me how to overcome this issue? My command line is below:

gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 6 -ref 
-sel -bin 0.5 -norm rdf


Akash
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[gmx-users] RDF Values

[Pandya, Akash]

Hi all,

I am calculating the RDF from a particular residue to a particular glycine 
molecule. I created an index file for both to do this. My simulation box is 
1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my 
trajectory and all the components stay inside the box. Please could someone 
tell me how to overcome this issue? My command line is below:

gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 6 -ref 
-sel -bin 0.5 -norm rdf


Akash
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Re: [gmx-users] RDF

[Saikat Pal]

Dear Vidya.R
Its very difficult to answer this question.It depends on your system .If you 
run more time of your system, RDF will be more smooth

Saikat Pal
IIT GUWAHATI



On Wednesday 12 July 2017, 10:02:30 AM IST, Vidya R  
wrote:

Hi,

I want to calculate RDF of my organic molecule with a solvent.

What should be the duration of my simulation?

Is 100 ps enough?


Thanks,
Vidya.R
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[gmx-users] RDF

[Vidya R]

Hi,

I want to calculate RDF of my organic molecule with a solvent.

What should be the duration of my simulation?

Is 100 ps enough?


Thanks,
Vidya.R
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Re: [gmx-users] RDF

[Justin Lemkul]

On 7/11/17 1:38 PM, Pandya, Akash wrote:

When I try to make an index group for the protein residue and the ligand 
molecule, the whole system is included in the index file.

I use these options:

r 166 (protein residue)

r 901 (ligand molecule)

then press q



All the default groups will still be there, you're just adding new ones into the 
list that you can choose from.  Neither of those will correspond to the whole 
system, so they should be viable choices at the gmx rdf prompt.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RDF

[Pandya, Akash]

When I try to make an index group for the protein residue and the ligand 
molecule, the whole system is included in the index file. 

I use these options:

r 166 (protein residue)

r 901 (ligand molecule)

then press q

Akash 

-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 Justin 
Lemkul
Sent: 11 July 2017 18:06
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] RDF



On 7/11/17 11:41 AM, Pandya, Akash wrote:
> Hi,
> 
> I want to calculate the RDF between a specific residue and a ligand molecule 
> in my simulation box. Is this possible and do I have to make a special index 
> group for that? If so how would I go about doing that?
> 

By using make_ndx or a suitable command-line selection when running gmx rdf 
(see gmx help selections, but make_ndx is often much easier to use/comprehend 
for very simple cases like this).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RDF

[Justin Lemkul]

On 7/11/17 11:41 AM, Pandya, Akash wrote:

Hi,

I want to calculate the RDF between a specific residue and a ligand molecule in 
my simulation box. Is this possible and do I have to make a special index group 
for that? If so how would I go about doing that?



By using make_ndx or a suitable command-line selection when running gmx rdf (see 
gmx help selections, but make_ndx is often much easier to use/comprehend for 
very simple cases like this).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] RDF

[Pandya, Akash]

Hi,

I want to calculate the RDF between a specific residue and a ligand molecule in 
my simulation box. Is this possible and do I have to make a special index group 
for that? If so how would I go about doing that?


Thanks,

Akash
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[gmx-users] RDF OF PROTEIN - LIGAND

[Neha Gupta]

Hi,

After simulations, can we plot the rdf of protein and ligand interaction?
How to refine the analysis?

Can anyone suggest suitable books / papers to interpret protein ligand
radial distribution funtion?

Thanks,
Neha
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Re: [gmx-users] RDF of a group around CNT axis

[Sajjad Kavyani]

I noticed that the gmx rdf some how cannot find the center of mass (COM)
for the CNT because after that I manually put a single particle in the COM
of the CNT and calculated the rdf around it (with -xy option), the gmx rdf
resulted the expected value which is a sharp peak at the radius of the cnt.
I tested all the -selrpos arguments but none of them could find the COM of
the CNT
Could you please help me to manage the problem ?

Regards
Sajjad

On Wed, Jun 7, 2017 at 7:19 PM, Sajjad Kavyani 
wrote:

> Dear Srinivas,
> That's absolutely right, I want to calculate the RDF of a certain
> group around the central axis of a nanotube.
> And as I know that the RDF of the CNT around its axis is just a sharp peak
> at the radius, I just tested the command-line parameters for this case, to
> specify that which command-line should be used.
>
> And honestly I do not understand the last sentence of your reply, could
> you please specify that after isolating the desired group, what
> command-line I should use?
>
> Sincerely,
> Sajjad
>
>
>
> On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI <
> scm...@scarletmail.rutgers.edu> wrote:
>
>> If I understand you correctly: you want to calculate the RDF of a certain
>> group (NOT part of the nanotube) around the central axis of a nanotube?
>>
>> The way I do these calculations is to use the gmx trjconv tool to isolate
>> a
>> trajectory file of ONLY the gropus I am interested in and run my
>> calculations on that.
>> If you expect to see one peak but see many that might mean that the RDF is
>> picking up groups that you don't want it to.
>>
>> Hope that helps,
>> Srinivas
>>
>> On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
>> wrote:
>>
>> > Dear experts,
>> > I want to calculate rdf of a certain group around the axis of a cnt,
>> but I
>> > do not know what are the proper parameters to choose in the
>> command-line.
>> > To test the parameters, I calculated the rdf of cnt itself around its
>> axis
>> > which must be a sharp peak at the cnt radius.
>> > I tested the following: (both selection groups of reference and rdf are
>> > CNT)
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
>> >
>> > BUT all the results are the same!!! and surprisingly they have multiple
>> > sharp peaks at different ranges, which I expected just one peak at the
>> > radius of the CNT 
>> > It is notable that the CNT is aligned to z axis.
>> > (the first two peaks are listed below):
>> >
>> >   0.000 211939.438
>> >   0.002 53771.996
>> >   0.004 11278.401
>> >   0.006 3935.633
>> >   0.008 1782.280
>> >   0.010  809.616
>> >   0.012  584.723
>> >   0.014  536.531
>> >   0.016  292.361
>> >   0.018  149.929
>> >   0.020   94.455
>> >   0.022   00.000
>> >   ...
>> >   ...
>> >   ...
>> >   0.11800.000
>> >   0.1200.375
>> >   0.1222.212
>> >   0.1240.725
>> >   0.1266.069
>> >   0.128   36.545
>> >   0.130  114.868
>> >   0.132  278.390
>> >   0.134 1669.916
>> >   0.136 2360.069
>> >   0.138  346.139
>> >   0.140  183.770
>> >   0.142   39.277
>> >
>> > Could you please explain to me that what should I do?
>> > --
>> > Gromacs Users mailing list
>> >
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>> > Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] RDF of a group around CNT axis

[Sajjad Kavyani]

Dear Srinivas,
That's absolutely right, I want to calculate the RDF of a certain
group around the central axis of a nanotube.
And as I know that the RDF of the CNT around its axis is just a sharp peak
at the radius, I just tested the command-line parameters for this case, to
specify that which command-line should be used.

And honestly I do not understand the last sentence of your reply, could you
please specify that after isolating the desired group, what command-line I
should use?

Sincerely,
Sajjad



On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI <
scm...@scarletmail.rutgers.edu> wrote:

> If I understand you correctly: you want to calculate the RDF of a certain
> group (NOT part of the nanotube) around the central axis of a nanotube?
>
> The way I do these calculations is to use the gmx trjconv tool to isolate a
> trajectory file of ONLY the gropus I am interested in and run my
> calculations on that.
> If you expect to see one peak but see many that might mean that the RDF is
> picking up groups that you don't want it to.
>
> Hope that helps,
> Srinivas
>
> On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
> wrote:
>
> > Dear experts,
> > I want to calculate rdf of a certain group around the axis of a cnt, but
> I
> > do not know what are the proper parameters to choose in the command-line.
> > To test the parameters, I calculated the rdf of cnt itself around its
> axis
> > which must be a sharp peak at the cnt radius.
> > I tested the following: (both selection groups of reference and rdf are
> > CNT)
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
> >
> > BUT all the results are the same!!! and surprisingly they have multiple
> > sharp peaks at different ranges, which I expected just one peak at the
> > radius of the CNT 
> > It is notable that the CNT is aligned to z axis.
> > (the first two peaks are listed below):
> >
> >   0.000 211939.438
> >   0.002 53771.996
> >   0.004 11278.401
> >   0.006 3935.633
> >   0.008 1782.280
> >   0.010  809.616
> >   0.012  584.723
> >   0.014  536.531
> >   0.016  292.361
> >   0.018  149.929
> >   0.020   94.455
> >   0.022   00.000
> >   ...
> >   ...
> >   ...
> >   0.11800.000
> >   0.1200.375
> >   0.1222.212
> >   0.1240.725
> >   0.1266.069
> >   0.128   36.545
> >   0.130  114.868
> >   0.132  278.390
> >   0.134 1669.916
> >   0.136 2360.069
> >   0.138  346.139
> >   0.140  183.770
> >   0.142   39.277
> >
> > Could you please explain to me that what should I do?
> > --
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Re: [gmx-users] RDF of a group around CNT axis

[SRINIVAS MUSHNOORI]

If I understand you correctly: you want to calculate the RDF of a certain
group (NOT part of the nanotube) around the central axis of a nanotube?

The way I do these calculations is to use the gmx trjconv tool to isolate a
trajectory file of ONLY the gropus I am interested in and run my
calculations on that.
If you expect to see one peak but see many that might mean that the RDF is
picking up groups that you don't want it to.

Hope that helps,
Srinivas

On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
wrote:

> Dear experts,
> I want to calculate rdf of a certain group around the axis of a cnt, but I
> do not know what are the proper parameters to choose in the command-line.
> To test the parameters, I calculated the rdf of cnt itself around its axis
> which must be a sharp peak at the cnt radius.
> I tested the following: (both selection groups of reference and rdf are
> CNT)
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
>
> BUT all the results are the same!!! and surprisingly they have multiple
> sharp peaks at different ranges, which I expected just one peak at the
> radius of the CNT 
> It is notable that the CNT is aligned to z axis.
> (the first two peaks are listed below):
>
>   0.000 211939.438
>   0.002 53771.996
>   0.004 11278.401
>   0.006 3935.633
>   0.008 1782.280
>   0.010  809.616
>   0.012  584.723
>   0.014  536.531
>   0.016  292.361
>   0.018  149.929
>   0.020   94.455
>   0.022   00.000
>   ...
>   ...
>   ...
>   0.11800.000
>   0.1200.375
>   0.1222.212
>   0.1240.725
>   0.1266.069
>   0.128   36.545
>   0.130  114.868
>   0.132  278.390
>   0.134 1669.916
>   0.136 2360.069
>   0.138  346.139
>   0.140  183.770
>   0.142   39.277
>
> Could you please explain to me that what should I do?
> --
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[gmx-users] RDF of a group around CNT axis

[Sajjad Kavyani]

Dear experts,
I want to calculate rdf of a certain group around the axis of a cnt, but I
do not know what are the proper parameters to choose in the command-line.
To test the parameters, I calculated the rdf of cnt itself around its axis
which must be a sharp peak at the cnt radius.
I tested the following: (both selection groups of reference and rdf are CNT)
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com

BUT all the results are the same!!! and surprisingly they have multiple
sharp peaks at different ranges, which I expected just one peak at the
radius of the CNT 
It is notable that the CNT is aligned to z axis.
(the first two peaks are listed below):

  0.000 211939.438
  0.002 53771.996
  0.004 11278.401
  0.006 3935.633
  0.008 1782.280
  0.010  809.616
  0.012  584.723
  0.014  536.531
  0.016  292.361
  0.018  149.929
  0.020   94.455
  0.022   00.000
  ...
  ...
  ...
  0.11800.000
  0.1200.375
  0.1222.212
  0.1240.725
  0.1266.069
  0.128   36.545
  0.130  114.868
  0.132  278.390
  0.134 1669.916
  0.136 2360.069
  0.138  346.139
  0.140  183.770
  0.142   39.277

Could you please explain to me that what should I do?
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[gmx-users] RDF calculation

[Farrokh Yousefi]

Dear gmx-users,

I am new to Gromacs. I have a droplet including some types of lipids such
as DPPC. I want to calculate RDF for head atom of DPPC with respect to
droplet center-of-mass. My question is how can i calculate this issue in
versions 2017. Apparently this feature has been removed from current
version (5.1.x). Please help me.

Thanks
Farrokh
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[gmx-users] rdf calculation with respect to center of mass

[Maryam Khalkhali]

Dear gmx-users,

The radial distribution function with respect to center-of-mass was computable 
in old gromacs versions. How can I calculate that  in newer version(2016)?
Thanks in advance.

Maryam
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Re: [gmx-users] RDF convergence

[Vitaly V. Chaban]

Mine converges.

What about box size?





On Fri, Dec 4, 2015 at 7:14 AM, Sudip Das  wrote:

> Hi,
>
> I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow:
>
> g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn
>
> But the rdf is not getting converged to 1 exactly, rather it converges to
> approximately 1.03. Whenever I am calculating rdf like this for different
> sets of atoms, I am getting the same thing.
>
> Can anyone please tell me why is this happening and what is the way out?
> Any kind of help will be highly appreciated.
>
> Thanks in advanced,
>
> Sudip
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[gmx-users] RDF convergence

[Sudip Das]

Hi,

I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow:

g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn

But the rdf is not getting converged to 1 exactly, rather it converges to
approximately 1.03. Whenever I am calculating rdf like this for different
sets of atoms, I am getting the same thing.

Can anyone please tell me why is this happening and what is the way out?
Any kind of help will be highly appreciated.

Thanks in advanced,

Sudip
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[gmx-users] RDF com

[Deva Priya]

Hello,

I am trying to calculate the rdf using the center of mass of a sulfonate
group, SO3 with other SO3 groups in the system. The SO3 group is part of a
bigger molecule. Is it appropriate to use

gmx rdf -rdf mol_com to carry out this operation or  should I use the

gmx rdf -yescom

In each case I would specify the group that contains SO3 atoms twice for
the rdf calculation.

Thanks for your help,

Deva
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Re: [gmx-users] RDF com

[Deva Priya]

Thanks a lot, Justin.

On Sat, Oct 17, 2015 at 8:02 AM, Justin Lemkul  wrote:

>
>
> On 10/17/15 5:32 AM, Deva Priya wrote:
>
>> Hello,
>>
>> I am trying to calculate the rdf using the center of mass of a sulfonate
>> group, SO3 with other SO3 groups in the system. The SO3 group is part of a
>> bigger molecule. Is it appropriate to use
>>
>> gmx rdf -rdf mol_com to carry out this operation or  should I use the
>>
>>
> This is correct.
>
> gmx rdf -yescom
>>
>>
> Boolean options are never prefixed with "yes" so you would have gotten an
> obvious fatal error here.
>
> In each case I would specify the group that contains SO3 atoms twice for
>> the rdf calculation.
>>
>>
> Yes.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] RDF com

[Justin Lemkul]

On 10/17/15 5:32 AM, Deva Priya wrote:

Hello,

I am trying to calculate the rdf using the center of mass of a sulfonate
group, SO3 with other SO3 groups in the system. The SO3 group is part of a
bigger molecule. Is it appropriate to use

gmx rdf -rdf mol_com to carry out this operation or  should I use the



This is correct.


gmx rdf -yescom



Boolean options are never prefixed with "yes" so you would have gotten an 
obvious fatal error here.



In each case I would specify the group that contains SO3 atoms twice for
the rdf calculation.



Yes.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RDF

[V.V.Chaban]

Search for my papers Vitaly V. Chaban. You will find many papers
determining solvation/solubility, where it is described how solubility
can be obtained from atomistic simulations.

RDF alone is not a proper descriptor. However, if you plot COM-COM RDF
for C60, you will get some solubility related information (but not
numerical solubility).

In my personal opinion, even with what you call binders solubility of
C60 is water is small. You will not be able to record it using small
MD systems.

Best of luck.




On Sat, Jul 18, 2015 at 7:08 AM, soumadwip ghosh
soumadwipgh...@gmail.com wrote:
 Dear all,
 I have attempted to show the dynamics of a C60 molecule in
 presence of aqueous soluble binders. I am using GROMOS53A6 force field and
 SPC/E water. I took the pdb as well as the itp file of both from the ATB
 server. I ran simulations using GROMACS 4.5.6 of fullerene both in presence
 and absence of the organic binders for 70 ns. In order to see whether
 fullerene becomes water dispersible or not I have planned to to calculate
 delta G solvation for both the cases using the thermodynamic integration
 method. But as of now, if in presence of a binder fullerene is more water
 soluble as compared to its pristine form this should be reflected in the
 RDF calculation between fullerene center of mass and Oxygen atoms fro water
 but as you can show in the link below, the reverse thing is happening.
 Link
 https://drive.google.com/file/d/0B7SBnQ5YXQSLVFY0MEItUTAzY1E/view?usp=sharing
 Is there something wrong with my approach. FYI I took 8 SDS binders which
 wraps around the fullerene molecule. I think I am missing out something
 very trivial.

 Any kind of help will be appreciated.

 Soumadwip Ghosh
 Research Fellow
 IITB
 India
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[gmx-users] RDF

[soumadwip ghosh]

Dear all,
I have attempted to show the dynamics of a C60 molecule in
presence of aqueous soluble binders. I am using GROMOS53A6 force field and
SPC/E water. I took the pdb as well as the itp file of both from the ATB
server. I ran simulations using GROMACS 4.5.6 of fullerene both in presence
and absence of the organic binders for 70 ns. In order to see whether
fullerene becomes water dispersible or not I have planned to to calculate
delta G solvation for both the cases using the thermodynamic integration
method. But as of now, if in presence of a binder fullerene is more water
soluble as compared to its pristine form this should be reflected in the
RDF calculation between fullerene center of mass and Oxygen atoms fro water
but as you can show in the link below, the reverse thing is happening.
Link
https://drive.google.com/file/d/0B7SBnQ5YXQSLVFY0MEItUTAzY1E/view?usp=sharing
Is there something wrong with my approach. FYI I took 8 SDS binders which
wraps around the fullerene molecule. I think I am missing out something
very trivial.

Any kind of help will be appreciated.

Soumadwip Ghosh
Research Fellow
IITB
India
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Re: [gmx-users] RDF

[André Farias de Moura]

you cannot predict solubility using the radial distribution of solvent
molecules around a single solute, single molecules just cannot aggregate
into a separate phase, so your system is too simple to provide the
information you want. even if you succeed in the thermodynamic integration,
it will provide you information about the transfer process of a single C60
from vacuum to the aqueous solution, but you would not be able to know
whether or not two or more C60 molecules would aggregate and would
eventually lead the system to a phase separation.

I'd suggest you either performing an equilibrium MD with a very large model
system with plenty of C60 molecules or an umbrella sampling simulation
using just a pair of molecules. In either case you would be assessing the
correlation between at least two C60 molecules and different PMF profiles
should provide sound arguments regarding the stabilization of the
hydrophobic solutes by the SDS molecules.

you might want to take a look at our recent paper and references therein:

de Moura et al., Thermodynamic Insights into the Self-Assembly of Capped
Nanoparticles using Molecular Dynamic Simulations, Physical Chemistry
Chemical Physics. 12/2014; 17(5). DOI: 10.1039/C4CP03519D

On Sat, Jul 18, 2015 at 7:08 AM, soumadwip ghosh soumadwipgh...@gmail.com
wrote:

 Dear all,
 I have attempted to show the dynamics of a C60 molecule in
 presence of aqueous soluble binders. I am using GROMOS53A6 force field and
 SPC/E water. I took the pdb as well as the itp file of both from the ATB
 server. I ran simulations using GROMACS 4.5.6 of fullerene both in presence
 and absence of the organic binders for 70 ns. In order to see whether
 fullerene becomes water dispersible or not I have planned to to calculate
 delta G solvation for both the cases using the thermodynamic integration
 method. But as of now, if in presence of a binder fullerene is more water
 soluble as compared to its pristine form this should be reflected in the
 RDF calculation between fullerene center of mass and Oxygen atoms fro water
 but as you can show in the link below, the reverse thing is happening.
 Link
 
 https://drive.google.com/file/d/0B7SBnQ5YXQSLVFY0MEItUTAzY1E/view?usp=sharing
 
 Is there something wrong with my approach. FYI I took 8 SDS binders which
 wraps around the fullerene molecule. I think I am missing out something
 very trivial.

 Any kind of help will be appreciated.

 Soumadwip Ghosh
 Research Fellow
 IITB
 India
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[gmx-users] RDF for molecules above a surface

[Jingjie Yeo (IHPC)]

Dear all,

I would like to find out the distribution of molecules above a flat surface, 
such as the surface of a membrane. Would it be appropriate to be using:
gmx rdf -f run.xtc -s run.tpr -n index.ndx -surf mol -rdf mol_com -pbc

After staring at the manual for really long, I can't quite figure out what 
exactly is the quantity that will be output. Is it correct to say that this is 
some kind of non-normalized distribution of the centre of mass of my chosen set 
of molecules from the surface of the membrane?

Best Regards,
JJ
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Re: [gmx-users] RDF

[mah maz]

Thanks Justin! I cant find so much details in the manual; there are only
general facts. does g_density give partial density?


On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote:

 Hi Justin
 The fact is I want to calculate water density in the system. If I select
 group1: oxygen and group2: oxygen, g_rdf command gives me very large
 numbers. Is it the number of atoms that should be changed to g/cm3?
 Besides, what does it calculate, each O is a reference atom during
 calculation?
 Thanks a lot!

 On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote:

 Dear all,
 I want to calculate the radial distribution function of water molecules
 in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers
 which is not logical I suppose. Is it meaningful if I separate oxygen and
 hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
 reference atom necessary to get RDF?
 Thanks!



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Re: [gmx-users] RDF

[Justin Lemkul]

On 5/19/15 4:12 AM, mah maz wrote:

Thanks Justin! I cant find so much details in the manual; there are only
general facts. does g_density give partial density?



Read the first sentence of the help description :)

-Justin



On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote:


Hi Justin
The fact is I want to calculate water density in the system. If I select
group1: oxygen and group2: oxygen, g_rdf command gives me very large
numbers. Is it the number of atoms that should be changed to g/cm3?
Besides, what does it calculate, each O is a reference atom during
calculation?
Thanks a lot!

On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote:


Dear all,
I want to calculate the radial distribution function of water molecules
in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers
which is not logical I suppose. Is it meaningful if I separate oxygen and
hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
reference atom necessary to get RDF?
Thanks!






--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] RDF

[mah maz]

Hi Justin
The fact is I want to calculate water density in the system. If I select
group1: oxygen and group2: oxygen, g_rdf command gives me very large
numbers. Is it the number of atoms that should be changed to g/cm3?
Besides, what does it calculate, each O is a reference atom during
calculation?
Thanks a lot!

On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote:

 Dear all,
 I want to calculate the radial distribution function of water molecules in
 my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which
 is not logical I suppose. Is it meaningful if I separate oxygen and
 hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
 reference atom necessary to get RDF?
 Thanks!

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Re: [gmx-users] RDF

[Justin Lemkul]

On 5/18/15 2:55 AM, mah maz wrote:

Hi Justin
The fact is I want to calculate water density in the system. If I select
group1: oxygen and group2: oxygen, g_rdf command gives me very large
numbers. Is it the number of atoms that should be changed to g/cm3?
Besides, what does it calculate, each O is a reference atom during
calculation?


All of this is in the manual.  The value of the RDF is the relative probability 
of finding a given particle as a function of distance.  If you just want 
density, there's a separate tool for that, conveniently called g_density.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] RDF

[mah maz]

Dear all,
I want to calculate the radial distribution function of water molecules in
my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which
is not logical I suppose. Is it meaningful if I separate oxygen and
hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
reference atom necessary to get RDF?
Thanks!
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Re: [gmx-users] RDF

[Justin Lemkul]

On 5/17/15 5:47 AM, mah maz wrote:

Dear all,
I want to calculate the radial distribution function of water molecules in
my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which
is not logical I suppose. Is it meaningful if I separate oxygen and
hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
reference atom necessary to get RDF?


RDF is always calculated relative to a reference, but the default behavior is to 
consider all atom pairs; see the manual.  It is generally standard practice in 
liquid RDF to separate out O-O vs. H-H etc.  There is even an example figure of 
this in the manual.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RDF plot with large g(r) values

[André Farias de Moura]

makes sense now, your system is quite heterogeneous.

you may use your RDF but some reviewers might not agree with this kind of
analysis for heterogeneous systems, so you have to explain why your
correlation peaks are so high and why the profiles don't converge to unity.

On Fri, Jan 9, 2015 at 12:34 AM, Kester Wong kester2...@ibs.re.kr wrote:

 Hi Andre,


 Thank you for your input.



 *보낸사람* : André Farias de Moura mo...@ufscar.br
 *받는사람* : Discussion list for GROMACS us gmx-us...@gromacs.org
 *받은날짜* : 2015년 1월 8일(목) 22:05:39
 *제목* : Re: [gmx-users] RDF plot with large g(r) values

 RDF values are sensitive to the volume of the system, so if you put the
 same solutes inside a larger/smaller box, RDF values change accordingly
 (check basic definitions of RDF in simulation handbooks to make sure you
 understand this relation).

 Ah right, that explains why my RDF values dropped if I put a larger amount
 of water in the same box.


 and even if you have the same size and composition, RDF may become really
 large if molecules aggregate.

 Yep, I have a droplet where the Na+ and OH- ions tend to aggregate within
 the solution, the high g(r) peak in the RDF almost doubles the other
 systems with no aggregation.
 In this case, can I still use my RDF plots?

 Regards,
 Kester


 On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong  wrote:

  Dear all,
 
 
 
  My apologies if this question sounds too basic of if it has been covered.
 
  I did some RDF calculations, and as when I plotted the figures, the g(r)
  values are in the hundreds, whereas the papers that I have seen are all in
  the range of 0-12.
 
  The x-axis (nm), however, seemed to be correct.
 
 
 
  Regards,
 
  Kester
 
 
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 Department of Chemistry
 Federal University of São Carlos
 São Carlos - Brazil
 phone: +55-16-3351-8090
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] RDF plot with large g(r) values

[Kester Wong]

Hi Andre,Thank you for your input.보낸사람 : "André Farias de Moura" mo...@ufscar.br받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2015년 1월 8일(목) 22:05:39제목 : Re: [gmx-users] RDF plot with large g(r) valuesRDF values are sensitive to the volume of the system, so if you put the
same solutes inside a larger/smaller box, RDF values change accordingly
(check basic definitions of RDF in simulation handbooks to make sure you
understand this relation).Ah right, that explains why my RDF values dropped if I put a larger amount of water in the same box.

and even if you have the same size and composition, RDF may become really
large if molecules aggregate.Yep, I have a droplet where the Na+ and OH- ions tend to aggregate within the solution, the high g(r) peak in the RDF almost doubles the other systems with no aggregation.In this case, can I still use my RDF plots?Regards,Kester
On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong <kester2...@ibs.re.kr> wrote:

 Dear all,



 My apologies if this question sounds too basic of if it has been covered.

 I did some RDF calculations, and as when I plotted the figures, the g(r)
 values are in the hundreds, whereas the papers that I have seen are all in
 the range of 0-12.

 The x-axis (nm), however, seemed to be correct.



 Regards,

 Kester


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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] RDF plot with large g(r) values

[Kester Wong]

Dear Justin, No, I am not comparing equivalent systems, nor reproducing previous findings. My simulation box contains a droplet of 2000 water molecules on graphene.The RDF of g(r) Ow-Ow shows a first peak at r = 0.3 nm, with a peak height of 400.For 6000 and 10,000 water molecules, the peak heights are 200 and 100, respectively. Is this due to the large vacuum in my simulation box?Regards,KesterOn 1/8/15 4:48 AM, Kester Wong wrote:
 Dear all,



 My apologies if this question sounds too basic of if it has been covered.

 I did some RDF calculations, and as when I plotted the figures, the g(r) values
 are in the hundreds, whereas the papers that I have seen are all in the range of
 0-12.


Are you comparing equivalent systems, e.g. trying to reproduce previous 
findings?  If not, it's just apples and oranges.  Your result is not necessarily 
unusual.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] RDF plot with large g(r) values

[Justin Lemkul]

On 1/8/15 4:48 AM, Kester Wong wrote:

Dear all,



My apologies if this question sounds too basic of if it has been covered.

I did some RDF calculations, and as when I plotted the figures, the g(r) values
are in the hundreds, whereas the papers that I have seen are all in the range of
0-12.



Are you comparing equivalent systems, e.g. trying to reproduce previous 
findings?  If not, it's just apples and oranges.  Your result is not necessarily 
unusual.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] RDF plot with large g(r) values

[André Farias de Moura]

RDF values are sensitive to the volume of the system, so if you put the
same solutes inside a larger/smaller box, RDF values change accordingly
(check basic definitions of RDF in simulation handbooks to make sure you
understand this relation).

and even if you have the same size and composition, RDF may become really
large if molecules aggregate.

On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong kester2...@ibs.re.kr wrote:

 Dear all,



 My apologies if this question sounds too basic of if it has been covered.

 I did some RDF calculations, and as when I plotted the figures, the g(r)
 values are in the hundreds, whereas the papers that I have seen are all in
 the range of 0-12.

 The x-axis (nm), however, seemed to be correct.



 Regards,

 Kester


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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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[gmx-users] RDF does not reach 1 for bulk

[Venkat Reddy]

Dear Gromacs users,

I would like to know why the normalized RDF data from g_rdf does not reach
1 for bulk?

As an alternative I tried using the raw data (i.e., by using the 'nonorm'
flag) and normalized the values by dividing them by  'rho*volume of bin',
which I believe is the standard method for normalization. Still I get the
trend obtained from the normalized data, where the end of the RDF curve
tapers downward, much below 1.

Kindly suggest how I could deal with this issue.

Thanks

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] RDF calculation.

[soumadwip ghosh]

Hi,
I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in terms of calculating the free energy
change.My question is-

1. while calculating radial distribution functions say between DNA minor
groove and choline, should I consider the center-off-mass atom of the minor
groove by using the -COM option of g_rdf?

2. Do you think calculation of PMF from g(r) for a specific ion binding
with the DNA can provide reliable free energy change or do I have to switch
to umbrella sampling?

PS: I only want to investigate the small molecule binding, not the
stability of the DNA duplex as a whole.

Thanks for your time in advance.

Soumadwip Ghosh
Research Fellow
Indian Institute of Technology Bombay
India
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Re: [gmx-users] RDF calculation.

[Marcelo Depólo]

Well, since you are not interested in the duplex stability, I would not use
-COM. See, during the simulation, the center-of-mass of such a small helix
part can drastically move, leading to a questionable result. Check your
system and make sure that you will not face this situation.

About the PMF, that depends on the ions you are using and the forcefields.
It is already known that some of them are poorly described, so check that
out too.

Hope it can help!
Cheers!

2014-12-27 7:17 GMT-02:00 soumadwip ghosh soumadwipgh...@gmail.com:

 Hi,
 I am studying the dynamics of a double stranded DNA in presence of
 small molecules. I want to study the preferential binding of these
 molecules in the grooves and backbones of the DNA and also calculate the
 feasibility of these binding in terms of calculating the free energy
 change.My question is-

 1. while calculating radial distribution functions say between DNA minor
 groove and choline, should I consider the center-off-mass atom of the minor
 groove by using the -COM option of g_rdf?

 2. Do you think calculation of PMF from g(r) for a specific ion binding
 with the DNA can provide reliable free energy change or do I have to switch
 to umbrella sampling?

 PS: I only want to investigate the small molecule binding, not the
 stability of the DNA duplex as a whole.

 Thanks for your time in advance.

 Soumadwip Ghosh
 Research Fellow
 Indian Institute of Technology Bombay
 India
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Re: [gmx-users] RDF calculation.

[Justin Lemkul]

On 12/27/14 4:17 AM, soumadwip ghosh wrote:

Hi,
 I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in terms of calculating the free energy
change.My question is-

1. while calculating radial distribution functions say between DNA minor
groove and choline, should I consider the center-off-mass atom of the minor
groove by using the -COM option of g_rdf?



I'm not sure it's useful.  Choline is a rather flexible molecule, so simply 
considering the COM of the minor groove vs. all atoms of choline is probably 
going to give you a very noisy profile.



2. Do you think calculation of PMF from g(r) for a specific ion binding
with the DNA can provide reliable free energy change or do I have to switch
to umbrella sampling?



This doesn't generally work well for ions, but the quality depends on the force 
field.  Depending on what the ion is, the exchange rate may be impossible to 
observe in an atomistic simulation.  The exchange rates for most common ions can 
range from nanosecond (feasible with MD) to microsecond (not reasonable, even if 
the force field is very accurate).


-Justin


PS: I only want to investigate the small molecule binding, not the
stability of the DNA duplex as a whole.

Thanks for your time in advance.

Soumadwip Ghosh
Research Fellow
Indian Institute of Technology Bombay
India



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] RDF analysis with respect to center of mass of rotein

[Justin Lemkul]

On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:

Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule)  i got a huge pick at 0.022 nm, 
which doesn’t make any sense (because i presumed that at this distance there 
must be a steric effect) am i right? Because this is my first time considering 
the center of mass of a molecule, so i don’t really know which distances are 
‘normal’ are which are not considering one group as a COM of the protein.

i used the next command:


g_rdf -f npt_production.xtc -com -s npt_production.tpr-o TEST-glycerol.xvg



group 1: Protein
group 2: GOL (glycerol molecules)



Indeed a distance of 0.022 nm would be physically impossible (that's 1/5 the 
length of a C-H bond!), so it's something else.  I wouldn't expect it to be an 
issue, but note that g_rdf warns about the value of nrexcl in the topology. 
Probably some intramolecular terms are contributing in a weird way.  If this is 
the only bizarre peak, you can probably safely ignore it using g_rdf -cut 0.05 
or something similar.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Carlos Navarro Retamal]

I Justin,
Thanks for your reply.
Sadly, that’s not the only bizarre peak,as you can see on the next image:
http://cl.ly/1B3B2y3I0o1R
This is how it looks when i don’t consideren the COM as a reference:
http://cl.ly/3m0d2W2y0N1Y
What; i your opinion,  could be the problem?
I think i’ll just have to use the second image to show the RDF.
Thanks a lot for your valuable help,
Best Regards,
Carlos


--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Friday, September 19, 2014 at 5:35 PM, Justin Lemkul wrote:

  
  
 On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
  Hi Justin,
  First of all thanks for your reply.
  It worked, but i’m getting weird results.
  When i measured the RDF between:
  Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 
  nm, which doesn’t make any sense (because i presumed that at this distance 
  there must be a steric effect) am i right? Because this is my first time 
  considering the center of mass of a molecule, so i don’t really know which 
  distances are ‘normal’ are which are not considering one group as a COM of 
  the protein.
   
  i used the next command:
   
   g_rdf -f npt_production.xtc -com -s npt_production.tpr-o TEST-glycerol.xvg
   
  group 1: Protein
  group 2: GOL (glycerol molecules)
   
  
  
 Indeed a distance of 0.022 nm would be physically impossible (that's 1/5 the  
 length of a C-H bond!), so it's something else. I wouldn't expect it to be an 
  
 issue, but note that g_rdf warns about the value of nrexcl in the topology.  
 Probably some intramolecular terms are contributing in a weird way. If this 
 is  
 the only bizarre peak, you can probably safely ignore it using g_rdf -cut 
 0.05  
 or something similar.
  
 -Justin
  
 --  
 ==
  
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
  
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
  
 jalem...@outerbanks.umaryland.edu (mailto:jalem...@outerbanks.umaryland.edu) 
 | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
  
 ==
 --  
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Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Justin Lemkul]

On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote:

I Justin,
Thanks for your reply.
Sadly, that’s not the only bizarre peak,as you can see on the next image:
http://cl.ly/1B3B2y3I0o1R
This is how it looks when i don’t consideren the COM as a reference:
http://cl.ly/3m0d2W2y0N1Y
What; i your opinion,  could be the problem?


No idea, aside from the nrexcl issue I mentioned before.  I don't know exactly 
why that would be a problem, but that's all I could suggest.  Has the trajectory 
been manipulated in any way, e.g. with trjconv?


-Justin


I think i’ll just have to use the second image to show the RDF.
Thanks a lot for your valuable help,
Best Regards,
Carlos


--
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile
Teléfono: 56-71-201 798,
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Friday, September 19, 2014 at 5:35 PM, Justin Lemkul wrote:




On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:

Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm, 
which doesn’t make any sense (because i presumed that at this distance there 
must be a steric effect) am i right? Because this is my first time considering 
the center of mass of a molecule, so i don’t really know which distances are 
‘normal’ are which are not considering one group as a COM of the protein.

i used the next command:


g_rdf -f npt_production.xtc -com -s npt_production.tpr-o TEST-glycerol.xvg


group 1: Protein
group 2: GOL (glycerol molecules)




Indeed a distance of 0.022 nm would be physically impossible (that's 1/5 the
length of a C-H bond!), so it's something else. I wouldn't expect it to be an
issue, but note that g_rdf warns about the value of nrexcl in the topology.
Probably some intramolecular terms are contributing in a weird way. If this is
the only bizarre peak, you can probably safely ignore it using g_rdf -cut 0.05
or something similar.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu (mailto:jalem...@outerbanks.umaryland.edu) | 
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Carlos Navarro Retamal]

Not at all. I’m using the .xtc file that comes from the simulation.
What do you mean with the nrexcl issue? Is there a way i can fix it?


--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Friday, September 19, 2014 at 6:21 PM, Justin Lemkul wrote:

  
  
 On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote:
  I Justin,
  Thanks for your reply.
  Sadly, that’s not the only bizarre peak,as you can see on the next image:
  http://cl.ly/1B3B2y3I0o1R
  This is how it looks when i don’t consideren the COM as a reference:
  http://cl.ly/3m0d2W2y0N1Y
  What; i your opinion, could be the problem?
   
  
  
 No idea, aside from the nrexcl issue I mentioned before. I don't know exactly 
  
 why that would be a problem, but that's all I could suggest. Has the 
 trajectory  
 been manipulated in any way, e.g. with trjconv?
  
 -Justin
  
  I think i’ll just have to use the second image to show the RDF.
  Thanks a lot for your valuable help,
  Best Regards,
  Carlos
   
   
  --
  Carlos Navarro Retamal
  Bioinformatic engineer
  Ph.D(c) in Applied Science, Universidad de Talca, Chile
  Center of Bioinformatics and Molecular Simulations (CBSM)
  Universidad de Talca
  2 Norte 685, Casilla 721, Talca - Chile
  Teléfono: 56-71-201 798,
  Fax: 56-71-201 561
  Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or 
  cnava...@utalca.cl (mailto:cnava...@utalca.cl)
   
   
  On Friday, September 19, 2014 at 5:35 PM, Justin Lemkul wrote:
   


   On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 
0.022 nm, which doesn’t make any sense (because i presumed that at this 
distance there must be a steric effect) am i right? Because this is my 
first time considering the center of mass of a molecule, so i don’t 
really know which distances are ‘normal’ are which are not considering 
one group as a COM of the protein.
 
i used the next command:
 
 g_rdf -f npt_production.xtc -com -s npt_production.tpr-o 
 TEST-glycerol.xvg
 
group 1: Protein
group 2: GOL (glycerol molecules)
 



   Indeed a distance of 0.022 nm would be physically impossible (that's 1/5 
   the
   length of a C-H bond!), so it's something else. I wouldn't expect it to 
   be an
   issue, but note that g_rdf warns about the value of nrexcl in the 
   topology.
   Probably some intramolecular terms are contributing in a weird way. If 
   this is
   the only bizarre peak, you can probably safely ignore it using g_rdf -cut 
   0.05
   or something similar.

   -Justin

   --
   ==

   Justin A. Lemkul, Ph.D.
   Ruth L. Kirschstein NRSA Postdoctoral Fellow

   Department of Pharmaceutical Sciences
   School of Pharmacy
   Health Sciences Facility II, Room 601
   University of Maryland, Baltimore
   20 Penn St.
   Baltimore, MD 21201

   jalem...@outerbanks.umaryland.edu 
   (mailto:jalem...@outerbanks.umaryland.edu) | (410) 706-7441
   http://mackerell.umaryland.edu/~jalemkul

   ==
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   send a mail to gmx-users-requ...@gromacs.org 
   (mailto:gmx-users-requ...@gromacs.org).

   
   
  
  
 --  
 ==
  
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
  
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
  
 jalem...@outerbanks.umaryland.edu (mailto:jalem...@outerbanks.umaryland.edu) 
 | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
  
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* Please 

Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Carlos Navarro Retamal]

Hi Justin,
Thanks again for all your help.  
If the problem is related to periodicity, why if i consider the whole protein i 
got ‘normal’ results?
In any case i centered the protein with the following command:


 trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o 
 traj_center.xtc
  
  
  

and then i measure the RDF with the following one:
 g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o 
 TEST-carbons.xvg

But i’m still seeing these weirds peaks a short distance.
 Best regards,
Carlos
--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Friday, September 19, 2014 at 6:48 PM, Justin Lemkul wrote:

  
  
 On 9/19/14 5:39 PM, Carlos Navarro Retamal wrote:
  Not at all. I’m using the .xtc file that comes from the simulation.
  What do you mean with the nrexcl issue? Is there a way i can fix it?
   
  
  
 The g_rdf help text describes issues related to nrexcl, but probably it's  
 unrelated. I suspect you're probably getting issues related to periodicity,  
 since the COM of a protein broken across a box is coincident with the box  
 center, where you also have solvent. Remove periodicity and/or center the  
 protein in the box and re-run g_rdf.
  
 -Justin
  
 --  
 ==
  
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
  
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
  
 jalem...@outerbanks.umaryland.edu (mailto:jalem...@outerbanks.umaryland.edu) 
 | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
  
 ==
 --  
 Gromacs Users mailing list
  
 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
  
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Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Justin Lemkul]

On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:

Hi Justin,
Thanks again for all your help.
If the problem is related to periodicity, why if i consider the whole protein i 
got ‘normal’ results?


A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect 
the outcome.



In any case i centered the protein with the following command:



trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o 
traj_center.xtc





and then i measure the RDF with the following one:

g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o 
TEST-carbons.xvg


But i’m still seeing these weirds peaks a short distance.


Unlikely, but it could be related to nrexcl; that's what you should try next.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Marcelo Depólo]

Carlos,

You might want to try a PBC correction with -pbc nojump and another RDF
calculation with the corrected trajectory.

2014-09-19 19:10 GMT-03:00 Justin Lemkul jalem...@vt.edu:



 On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:

 Hi Justin,
 Thanks again for all your help.
 If the problem is related to periodicity, why if i consider the whole
 protein i got ‘normal’ results?


 A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't
 affect the outcome.

  In any case i centered the protein with the following command:


  trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o
 traj_center.xtc




 and then i measure the RDF with the following one:

 g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o
 TEST-carbons.xvg


 But i’m still seeing these weirds peaks a short distance.


 Unlikely, but it could be related to nrexcl; that's what you should try
 next.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 Gromacs Users mailing list

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 Support/Mailing_Lists/GMX-Users_List before posting!

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 send a mail to gmx-users-requ...@gromacs.org.




-- 
Marcelo Depólo Polêto
Biochemicist
University of Viçosa - Brazil
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Re: [gmx-users] RDF analysis with respect to center of mass of otein

[Carlos Navarro Retamal]

Hi Marcelo,
Thanks for your reply.
Sadly it didn’t work either, so i’m trying to generate a new .tpr file by 
changing the nrexcl values just as Justin suggest.
Hope this may works.
Thanks the two of you.
Best Regards,
Carlos


--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Friday, September 19, 2014 at 8:58 PM, Marcelo Depólo wrote:

 Carlos,
  
 You might want to try a PBC correction with -pbc nojump and another RDF
 calculation with the corrected trajectory.
  
 2014-09-19 19:10 GMT-03:00 Justin Lemkul jalem...@vt.edu 
 (mailto:jalem...@vt.edu):
  
   
   
  On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:
   
   Hi Justin,
   Thanks again for all your help.
   If the problem is related to periodicity, why if i consider the whole
   protein i got ‘normal’ results?

   
   
  A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't
  affect the outcome.
   
  In any case i centered the protein with the following command:


   trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o
traj_center.xtc

   and then i measure the RDF with the following one:

g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o
TEST-carbons.xvg
 


   But i’m still seeing these weirds peaks a short distance.
   
  Unlikely, but it could be related to nrexcl; that's what you should try
  next.
   
  -Justin
   
  --
  ==
   
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
   
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 601
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
   
  jalem...@outerbanks.umaryland.edu 
  (mailto:jalem...@outerbanks.umaryland.edu) | (410) 706-7441
  http://mackerell.umaryland.edu/~jalemkul
   
  ==
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 --  
 Marcelo Depólo Polêto
 Biochemicist
 University of Viçosa - Brazil
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[gmx-users] RDF analysis with respect to center of mass of Protein

[Carlos Navarro Retamal]

Dear gromacs users,
In order to measure the interactions between a Protein with respect to a 
mixture solvent solution  (glycerol-water) i’m trying to measure the RDF 
between the protein with respect to the C and O atoms of Glycerol respectively.
By now i have measured g(r) between:

Protein - Glycerol
Protein Backbone - Glycerol
SideChain - Glycerol

but sadly, because i’m considering a huge amount of atoms of the Protein, the 
RDF graphic doesn’t look that good.
On that way i thought that maybe a better approximation will be to measure the 
RDF between the center of Mass of the protein with respect to the glycerol 
molecules, but i don’t know how to use make_ndx to create such kind of group.
Is there a way to do this? Or maybe you may think in a better idea.
Hope someone can help me.
Best regards,
Carlos  

--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl

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Re: [gmx-users] RDF analysis with respect to center of mass of Protein

[Justin Lemkul]

On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:


Dear gromacs users,
In order to measure the interactions between a Protein with respect to a 
mixture solvent solution  (glycerol-water) i’m trying to measure the RDF 
between the protein with respect to the C and O atoms of Glycerol respectively.
By now i have measured g(r) between:

Protein - Glycerol
Protein Backbone - Glycerol
SideChain - Glycerol

but sadly, because i’m considering a huge amount of atoms of the Protein, the 
RDF graphic doesn’t look that good.
On that way i thought that maybe a better approximation will be to measure the 
RDF between the center of Mass of the protein with respect to the glycerol 
molecules, but i don’t know how to use make_ndx to create such kind of group.


It's not a task for make_ndx.  g_rdf does this with the -com option.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RDF analysis with respect to center of mass of rotein

[Carlos Navarro Retamal]

Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule)  i got a huge pick at 0.022 nm, 
which doesn’t make any sense (because i presumed that at this distance there 
must be a steric effect) am i right? Because this is my first time considering 
the center of mass of a molecule, so i don’t really know which distances are 
‘normal’ are which are not considering one group as a COM of the protein.

i used the next command:

 g_rdf -f npt_production.xtc -com -s npt_production.tpr-o TEST-glycerol.xvg  
  

group 1: Protein
group 2: GOL (glycerol molecules)



Thanks again for your valuable help,  
Best Regards,
Carlos
--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Thursday, September 18, 2014 at 4:10 PM, Justin Lemkul wrote:

  
  
 On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:
   
  Dear gromacs users,
  In order to measure the interactions between a Protein with respect to a 
  mixture solvent solution (glycerol-water) i’m trying to measure the RDF 
  between the protein with respect to the C and O atoms of Glycerol 
  respectively.
  By now i have measured g(r) between:
   
  Protein - Glycerol
  Protein Backbone - Glycerol
  SideChain - Glycerol
   
  but sadly, because i’m considering a huge amount of atoms of the Protein, 
  the RDF graphic doesn’t look that good.
  On that way i thought that maybe a better approximation will be to measure 
  the RDF between the center of Mass of the protein with respect to the 
  glycerol molecules, but i don’t know how to use make_ndx to create such 
  kind of group.
   
  
  
 It's not a task for make_ndx. g_rdf does this with the -com option.
  
 -Justin
  
 --  
 ==
  
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
  
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
  
 jalem...@outerbanks.umaryland.edu (mailto:jalem...@outerbanks.umaryland.edu) 
 | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
  
 ==
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Re: [gmx-users] RDF of solvation shell molecules

[Justin Lemkul]

On 5/23/14, 12:37 AM, sujithkakkat . wrote:

Hello Chandan,

  Thank you for the response.

   I have used g_rdf, but I guess it gives the RDF for the whole system.
Say, if I choose water oxygen, it will plot RDF from water molecules in the
whole system. But, I want the RDF for the solvation shell water molecules
,leaving the bulk water . I came across such a plot in an article where the
author studied the structure of solvation shell . So do you think it is
possible to do that GROMACS?



You already have it.  The first solvation shell is the first peak in the RDF.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] RDF of solvation shell molecules

[sujithkakkat .]

Hello,

I would like to know if it is possible to plot the RDF of water
molecules belonging to the solvation shell of a solute. I mean, I want to
know the effect of the solute on the water arrangement in the solvation
shell.  Is there a way to do this?

Regards,

Sujith.
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