[gmx-users] gmx rdf (Angular Dependence)

[Farag, Hossam Mostafa Abdelhamid Mostafa]

Hi,

In the 2020.1 Release of Gromacs Documentation, it is written in page 486 the 
following:

"With gmx rdf (page 135) it is also possible to calculate an angle dependent 
rdf g_AB(r, theta), where the angle theta is defined with respect to a certain 
laboratory axis e, see Fig. 5.50 B"

However, when I go to "gmx rdf" command, I can't find any options to compute 
the anisotropic distribution.

I only found an option called -xy, which I am not sure how to use if this is 
the one relevant to what I am looking for.

Looking forward for your help.
Many thanks!
Hossam Farag
Graduate Research Assistant

Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
3614 Beckman Institute
405 N. Mathews Ave.
Urbana, IL 61801
217.418.3196 | hfar...@illinois.edu

[cid:e3f6c7fd-050f-4257-b3e1-c9207270e649]
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[gmx-users] gmx rdf selrpos seltype

[Giuseppe R Del Sorbo]

Dear gmx users,

I am calculating a spherical radial distribution function between the 
center of mass of the methyl group of STS (my surfactant) around the 
center of mass of the STS micelle.


I am using this command:

gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr 
-selrpos whole_mol_com -seltype atom -b 8  -ref ST -sel C2 -o 
output.xvg


and I get my graph.

If I switch selrpose with seltype and I type:

gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr 
-seltype whole_mol_com -selrpose atom -b 8 -ref C2 -sel ST -o 
output.xvg


I get a different result.


If I well understood, in the first case the reference position is the 
center of mass the micelle


and in the second case the reference position is the methyl group.

Teorically I should get the same result, maybe there is something in 
selrpos and seltype which I missed.


Can anyone help me?

Thanks a lot

Giuseppe
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[gmx-users] gmx rdf with surf option

[zeineb SI CHAIB]

Dear GMX users,

I have a question regarding GMX RDF and I apologize if my question is too basic.

My trajectory consists of a dimer inserted in a membrane with an explicit 
water/ion environment. I would like to compute the distribution of the center 
of mass of lipid molecules to the surface of the receptor.

My first test consisted of the following command:

1) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_T1.xvg -surf  mol -seltype 
whole_res_com


I got the following error:

Inconsistency in user input: -surf only works with -ref that consists of atoms
When I run again the same command line but with -selrpos, it works "fine"
2) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_T1.xvg -surf mol -selrpos 
whole_res_com
I know that COMs are not supported with -surf. But -seltype is supposed to be 
related to "the type of selection for the atom or group, residue, etc, we want 
to calculate the rdf for" no?. I can't understand why I got this error when 
using -seltype with -surf option. Any comment on this?
In another test I tried this:
3) gmx rdf -f traj.xtc -s md.tpr -n index.ndx  -o rdf_g15.xvg -surf mol -ref 
'protein' -sel ''whole_res_com of group 15''
this one works fine but the output is different from the previous command (2). 
Although for me I was expecting the same results?!
If none of these commands is correct, can you please tell me which option I can 
use in order to compute the RDF as the distribution of COM of lipid molecules 
to the surface of the protein, please?
Thanks a lot.

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[gmx-users] gmx rdf not reading gmx checked trr file.

[Jones de Andrade]

Hi all.

I'm having a problem with gmx rdf in some trajectories of mine.

I'm dealing with several mixtures of two solvents in different concentrations. 
While I was dealing with the "non-infine dilutions", or when I had several 
molecules of each, gmx rdf calculated the rdfs with no error.

Now, I'm having the following error, only in trajectories where I have one 
molecule of one solvent and 999 of the other. I also would like to point out 
that I tested gmx check on the trajectories in question, with absolutely no 
failure identified in the trr files.

##

---
Program: gmx rdf, version 2018
Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 228)
Function:void gmx::TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()

System I/O error:
Could not read coordinates from trajectory

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

##

Does anybody have an idea on what is going wrong?

Thanks a lot in advance.
-- 
Jones de Andrade
(jdandr...@iq.ufrgs.br)
DFQ/IQ/UFRGS
Lattes: http://lattes.cnpq.br/6675936210583999
Orcid: https://orcid.org/-0003-3429-8119

Enviado pelo K-9 mail
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[gmx-users] gmx rdf

[Dhrubajyoti Maji]

Dear gromacs users,
 I have simulated a system of liquid acetamide in gromacs-2018.3 using
opls ff. I have calculated g(r) with gmx rdf. While O-O and com-com rdf are
similar as reported but N-O and O-H rdf are way different . I have tried
both aa and ua models but this problem persists. Other properties like
density,dipole moment, dielectric constant, diffusion coefficient matches
very well. Any suggestion will be highly appreciated.
Thanks and regards.
Dhrubajyoti Maji
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Re: [gmx-users] gmx rdf

[Justin Lemkul]

On 6/20/16 9:22 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello gmx_users,
I was trying to plot distribution function in a bilayer system using gmx
rdf. I used the system as a reference ( thinking it will take the COM of
the system as reference point) . Then I plotted RDF of a marked atom. But
it is plotting only in the positive direction while the lipids in the
lower leaflet are also containing the marked atom. So I am unable to see
the distribution from center of the bilayer to the lower leaflet.
Can anyone please help me out in identifying my mistake.



Distance is a positive value and that's what gmx rdf will always report.  If you 
want to distinguish between different leaflets, create an index file for the 
different leaflets; but gmx rdf will always report a positive number.


-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] gmx rdf

[amitbehra]

Hello gmx_users,
I was trying to plot distribution function in a bilayer system using gmx
rdf. I used the system as a reference ( thinking it will take the COM of
the system as reference point) . Then I plotted RDF of a marked atom. But
it is plotting only in the positive direction while the lipids in the
lower leaflet are also containing the marked atom. So I am unable to see
the distribution from center of the bilayer to the lower leaflet.
Can anyone please help me out in identifying my mistake.

Regards,
Amit Behera

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Re: [gmx-users] 'gmx rdf' and 'gmx select' questions

[Teemu Murtola]

Hi,

On Fri, May 27, 2016 at 9:19 PM Eric Smoll  wrote:

> (1) What is the difference between 'res' and 'mol' position specifiers? I
> assume 'res' refers the set of all atoms that have the same gro-file
> residue-number *and* residue name. Is this correct? What does 'mol'
> indicate?
>

You are correct about 'res': it refers to a residue, which is typically
inferred from residue numbers and names. 'mol' stands for molecule, and can
be used with .tpr input, where it refers to molecules specified in the
topology.


> (2) 'gmx rdf' in Gromacs 5.1.2 allows the user to specify the '-ref' and
> '-sel' groups with 'gmx select' style selection strings on the commandline.
> It appears that there is an option to provide selections from a file with
> the '-sf' flag. 'gmx help selections cmdline' suggests that  '-sf file.dat'
> should be provided as an argument to a selection. If the '-ref' and '-sel'
> groups are not identical, can this flag be used twice with two different
> files? For example:
>
> gmx rdf -ref -sf file1.dat -sel -sf file2.dat
>
> Is this correct?
>

Yes, this is correct. Also if the selections are identical, you can still
use the -sf flag twice, with the same file both times. It is also possible
to put both selections into the same file and just use -sf once, after both
options (like -ref -sel -sf file.dat).

Best regards,
Teemu
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[gmx-users] 'gmx rdf' and 'gmx select' questions

[Eric Smoll]

Hello Gromacs users,

I have a few syntax questions:

(1) What is the difference between 'res' and 'mol' position specifiers? I
assume 'res' refers the set of all atoms that have the same gro-file
residue-number *and* residue name. Is this correct? What does 'mol'
indicate?

(2) 'gmx rdf' in Gromacs 5.1.2 allows the user to specify the '-ref' and
'-sel' groups with 'gmx select' style selection strings on the commandline.
It appears that there is an option to provide selections from a file with
the '-sf' flag. 'gmx help selections cmdline' suggests that  '-sf file.dat'
should be provided as an argument to a selection. If the '-ref' and '-sel'
groups are not identical, can this flag be used twice with two different
files? For example:

gmx rdf -ref -sf file1.dat -sel -sf file2.dat

Is this correct?

Best
Eric
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Re: [gmx-users] gmx rdf gromacs 5.1 question!

[Teemu Murtola]

Hi,

indeed, this appears to be a bug, likely originating already from 5.0
times. I'll try to fix that soon. But it is just a convenience option,
anyways: you can always write each of your selections as "mol_com of ...",
and it should work the same.

Best regards,
Teemu

On Fri, Sep 25, 2015 at 11:50 AM Stelios Karozis <
skaro...@ipta.demokritos.gr> wrote:

> Hi Teemu
> Thanks for your response, but -seltype is not available as a flag for
> gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd (I gave
> it a try...)
>
> --
> Karozis Stelios
> Chemical Engineer, MSc
> Research Associate at EREL
> NCSR D- INRASTES
> tel:0030 210 650 3403
> e-mail: skaro...@ipta.demokritos.gr
>
>
> On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
>  wrote :
>
> > Hi,
> >
> > You should use -seltype instead of -selrpos in this case.
> >
> > Best regards,
> > Teemu
> >
> > On Fri, Sep 25, 2015, 11:12 Stelios Karozis
> >  wrote:
> >
> > > Greeting everyone,
> > > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > > command. With older version of gromacs I used -xy -rdf mol_com
> > >  flags. As far as I can understand, the equivalent flags for
> > > gromacs 5.1 are -xy -selrpos mol_com but the result is not correct.
> > > For instance the first peak is at 0nm and not close to 0.5nm...
> > > I believe I am not using the right flags.
> > >
> > > Thanks in advance for your help
> > >
> > > --
> > > Karozis Stelios
> > > Chemical Engineer, MSc
> > > Research Associate at EREL
> > > NCSR D- INRASTES
> > > tel:0030 210 650 3403
> > > e-mail: skaro...@ipta.demokritos.gr
> > > --
> > > 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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[gmx-users] gmx rdf gromacs 5.1 question!

[Stelios Karozis]

Greeting everyone,
I strated using gromacs 5.1 and I have difficulties with gmx rdf
command. With older version of gromacs I used -xy -rdf mol_com
 flags. As far as I can understand, the equivalent flags for gromacs 5.1
 are -xy -selrpos mol_com but the result is not correct. For instance
 the first peak is at 0nm and not close to 0.5nm...
I believe I am not using the right flags. 

Thanks in advance for your help

-- 
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr 
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Re: [gmx-users] gmx rdf gromacs 5.1 question!

[Teemu Murtola]

Hi,

You should use -seltype instead of -selrpos in this case.

Best regards,
Teemu

On Fri, Sep 25, 2015, 11:12 Stelios Karozis 
wrote:

> Greeting everyone,
> I strated using gromacs 5.1 and I have difficulties with gmx rdf
> command. With older version of gromacs I used -xy -rdf mol_com
>  flags. As far as I can understand, the equivalent flags for gromacs 5.1
>  are -xy -selrpos mol_com but the result is not correct. For instance
>  the first peak is at 0nm and not close to 0.5nm...
> I believe I am not using the right flags.
>
> Thanks in advance for your help
>
> --
> Karozis Stelios
> Chemical Engineer, MSc
> Research Associate at EREL
> NCSR D- INRASTES
> tel:0030 210 650 3403
> e-mail: skaro...@ipta.demokritos.gr
> --
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> posting!
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Re: [gmx-users] gmx rdf gromacs 5.1 question!

[Stelios Karozis]

Hi Teemu
Thanks for your response, but -seltype is not available as a flag for
gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd (I gave
it a try...)

-- 
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr 


On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
 wrote :

> Hi,
> 
> You should use -seltype instead of -selrpos in this case.
> 
> Best regards,
> Teemu
> 
> On Fri, Sep 25, 2015, 11:12 Stelios Karozis
>  wrote:
> 
> > Greeting everyone,
> > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > command. With older version of gromacs I used -xy -rdf mol_com
> >  flags. As far as I can understand, the equivalent flags for
> > gromacs 5.1 are -xy -selrpos mol_com but the result is not correct.
> > For instance the first peak is at 0nm and not close to 0.5nm...
> > I believe I am not using the right flags.
> >
> > Thanks in advance for your help
> >
> > --
> > Karozis Stelios
> > Chemical Engineer, MSc
> > Research Associate at EREL
> > NCSR D- INRASTES
> > tel:0030 210 650 3403
> > e-mail: skaro...@ipta.demokritos.gr
> > --
> > 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] gmx rdf gromacs 5.1 question!

[Stelios Karozis]

Thanks with selections syntax it works!


-- 
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr 


On Fri, 25 Sep 2015 12:05:41 +0300, "Teemu Murtola"
 wrote :

> Hi,
> 
> indeed, this appears to be a bug, likely originating already from 5.0
> times. I'll try to fix that soon. But it is just a convenience option,
> anyways: you can always write each of your selections as "mol_com
> of ...", and it should work the same.
> 
> Best regards,
> Teemu
> 
> On Fri, Sep 25, 2015 at 11:50 AM Stelios Karozis <
> skaro...@ipta.demokritos.gr> wrote:
> 
> > Hi Teemu
> > Thanks for your response, but -seltype is not available as a flag
> > for gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd
> > (I gave it a try...)
> >
> > --
> > Karozis Stelios
> > Chemical Engineer, MSc
> > Research Associate at EREL
> > NCSR D- INRASTES
> > tel:0030 210 650 3403
> > e-mail: skaro...@ipta.demokritos.gr
> >
> >
> > On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
> >  wrote :
> >
> > > Hi,
> > >
> > > You should use -seltype instead of -selrpos in this case.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Fri, Sep 25, 2015, 11:12 Stelios Karozis
> > >  wrote:
> > >
> > > > Greeting everyone,
> > > > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > > > command. With older version of gromacs I used -xy -rdf mol_com
> > > >  flags. As far as I can understand, the equivalent flags for
> > > > gromacs 5.1 are -xy -selrpos mol_com but the result is not
> > > > correct. For instance the first peak is at 0nm and not close to
> > > > 0.5nm... I believe I am not using the right flags.
> > > >
> > > > Thanks in advance for your help
> > > >
> > > > --
> > > > Karozis Stelios
> > > > Chemical Engineer, MSc
> > > > Research Associate at EREL
> > > > NCSR D- INRASTES
> > > > tel:0030 210 650 3403
> > > > e-mail: skaro...@ipta.demokritos.gr
> > > > --
> > > > Gromacs Users mailing list
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