Re: [gmx-users] question about make_ndx

[Ullmann, Thomas]

Hi,

Under Unix/Linux you can use

gmx make_ndx -f struc.gro -o test.ndx << _EOR_
r 1
q
_EOR_

Best,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Carlos Navarro 

Sent: Thursday, April 4, 2019 5:55:26 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] question about make_ndx

Dear gmx users,
I’m trying to feed make_ndx though echo, but I’m having some issues.
When I use echo  "r 1"  | gmx make_ndx -f struc.gro -o test.ndx I got the
following error message:

Fatal error:
Error reading user input

So apparently I have to include also the q argument to close properly
make_ndx, but I don’t know how to do this.
I have tried with echo  "r 1 q"  | gmx make_ndx, echo  "r 1” “q"  | gmx
make_ndx, and other combinations, but non of them worked.
Any ideas?
Best regards,
Carlos

——
Carlos Navarro Retamal
Bioinformatic Engineering. PhD.
Postdoctoral Researcher in Center of Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca, Chile
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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[gmx-users] Functional Mode Analysis (FMA)

[Ullmann, Thomas]

Hi Eduardo,

The FMA tool is not yet included  in the official distributed  GROMACS
version, but it is under code review. You can build GROMACS with the
FMA tool from the attached tar ball of the development version that is
currently being reviewed. The FMA tool can then be called as gmx fma
(see gmx fma -h for options).
The list doesn't accept attachments,  so I sent you the tar ball off-list.

Happy Computing,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
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Re: [gmx-users] Binding cavity analysis

[Ullmann, Thomas]

Hi,

I forwarded your email to the GROMACS users list,
please use it for user questions. In this way you
have a greater chance of getting answers and others
can find the questions and answers online.

>I have a 2 microsecond trajectory of protein-ligand system. I want to 
>calculate 3 things:
>
>1. Time series of number of water molecules in binding cavity.

Give gmx select a try. You could select water molecules within
a certain distance of atoms of cavity lining residues.

>2. Volume evolution of in the binding cavity.

There are a number of tools not distributed with GROMACS
that you could try, for example
trj_cavity 
https://sourceforge.net/projects/trjcavity/
and caver https://www.caver.cz

>3. Water surface density evolution in the cavity.

I'm not sure how you would define this quantity
but a combination of the select and sasa tools of
gmx may work.


Best,
Thomas.

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[gmx-users] FW: Binding cavity analysis

[Ullmann, Thomas]

From: Wycliffe Omwansu [womwa...@gmail.com]
Sent: Saturday, August 11, 2018 7:29 AM
To: Ullmann, Thomas
Subject: Binding cavity analysis

Hi,

I have a 2 microsecond trajectory of protein-ligand system. I want to calculate 
3 things:
1. Time series of number of water molecules in binding cavity.
2. Volume evolution of in the binding cavity.
3. Water surface density evolution in the cavity.

How can I go about it using gromacs?

Thank you.

Wycliffe
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Re: [gmx-users] Any update on constant pH simulation?

[Ullmann, Thomas]

Hi Jagannath,

The current implementation an older GROMACS version (3.3.1) can in principle be 
used, but is
slow for systems with many titratable sites na d has some other restrictions. 
You find it here:
http://www.mpibpc.mpg.de/grubmueller/constpH

The new constant pH framework will offer higher flexibility and performance but 
still need some
time. The project website can be found here:
http://www.mpibpc.mpg.de/grubmueller/sppexa

Best,
Thomas.


--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jagannath 
Mondal [jmondal.bac...@gmail.com]
Sent: Tuesday, August 23, 2016 6:41 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Any update on constant pH simulation?

Dear Gromacs users and developers
  Is there any new update on implementation of constant pH simulations on
recent gromacs version?
I am aware of the gromacs faq
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
But I wanted to check if there is any update on this ?
Jagannath
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Re: [gmx-users] fe4s4

[Ullmann, Thomas]

A good starting point to get an idea of the challenges posed by
iron sulfur clusters are the publications of Louis Noodleman.

Good luck,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Nilkanta 
Chowdhury [nil5...@gmail.com]
Sent: Saturday, May 28, 2016 2:19 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] fe4s4

will you please guide me. how can I do this?
On May 28, 2016 5:11 PM, "Justin Lemkul"  wrote:

>
>
> On 5/28/16 3:59 AM, Nilkanta Chowdhury wrote:
>
>> Hello friends,
>>   I want to simulate a protein  molecule boud with a
>> Fe4S4 molecule, in gromacs. How do i generet the topology og this fe4s4
>> molecule.
>>
>
> You need to obtain/derive parameters for it.  That's not a simple species
> to deal with.
>
> -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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>
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Re: [gmx-users] Nitrate parameters CHARMM

[Ullmann, Thomas]

Hi Tyler,

http://dx.doi.org/10.1002/smll.201102056

Best,
Thomas


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tyler Cropley 
[tyler.crop...@wagner.edu]
Sent: Thursday, February 18, 2016 8:44 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Nitrate parameters CHARMM

Dear Gromacs users,

We are trying to set up simulations using the nitrate anion. Unfortunately,
the CHARMM force field does not support nitrate. Does anyone know the
parameters needed or can point me to a paper that contains them.

Thank you!
Tyler Cropley
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Re: [gmx-users] trjcat

[Ullmann, Thomas]

Hi Elham,

use trjconv -dt NEW_TIME_STEP_IN_ps.

Happy simulating,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of elham tazikeh 
[elham.tazi...@gmail.com]
Sent: Sunday, September 20, 2015 9:00 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] trjcat

Dear GMX users
i ve simulated a system with 1500 steps in md.mdp file and every 3000
steps save the coordinations, thus we have 5000 frames
i know i should use *trjcat* for reduce my frames, but i dont know how?
for instance for reduction to 500 frames,
please guide me about that
regards
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Re: [gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series

[Ullmann, Thomas]

For the record, the problem of not getting the output expected from gmx distance
may have been related to a bug fixed here: https://gerrit.gromacs.org/#/c/4843/1

Happy computing,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham 
[mark.j.abra...@gmail.com]
Sent: Thursday, May 07, 2015 4:52 PM
To: oliwias; gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist
time series

Hi,

On Thu, May 7, 2015 at 3:59 PM oliwias  wrote:

> 1. How can I get rid of the inconsistency? Did I use the wrong options
> for gmx_trjcat?
>

Depends whether you care. You wrote files with two different output
periods, and now you want to treat them as a continuous thing, which in one
sense they are not. Whether that matters depends what you want to do next,
and that's your call. trjconv has functionality that would e.g. let you
extract only the frames from one set of trajectories that will match the
period of the other, and then you can trjcat the lot together.

You can also first get gmx distance working on your partial trajectories,
to solve that part of the problem independently.

2. About the distances - for gromacs 4.6.7 I used:
> printf "A\nB\n" | g_dist -s md_2.tpr -f md.xtc -n sys.ndx -o dist.xvg
> -dt 100
>
> for gromacs 5.0 I used:
> printf "A\nB\n" | gmx distance -s md_2.tpr -f md.xtc -n sys.ndx -oall
> dist_all.xvg -oav dist_av.xvg -oh dist_h.xvg -dt 100 -tu ns
>

You're doing two different things here. You've set the units with -tu to
ns, and so (IIRC) -dt is interpreted in that context. I don't know if
that's part of the problem.

More important is that you read gmx distance -h, compare with g_dist -h and
realise that the functionality in gmx distance is much greater than g_dist.
You need to use the selection syntax to get the COM for your two index
grounds, which g_dist did for you because that's all it could do.

Mark

Doees that indicate anything?
>
> Cheers,
> oliwia
>
> On 07.05.2015 15:43, Mark Abraham wrote:
> > Hi
> >
> > On Thu, May 7, 2015 at 3:34 PM oliwias  wrote:
> >
> >> Hi Mark,
> >>
> >> I'm quite new to gromacs, so thanks for your help! I have an md
> >> trajectory in 3 files. I used:
> >> gmx_trjcat -f md1.xtc md2.xtc md3.xtc -o md.xtc -settime
> >> in order to get one file for analysis. I set the time of the first
> >> file
> >> to 0.0, and for the next two files I set the time to "c" (continue, I
> >> suppose). When I run:
> >> gmx check -f md.xtc -s1 md_2.tpr -c
> >> I get a message:
> >> "Timesteps at t=2 don't match (2, 5)"
> >>
> >> I don't know why... The only reason that comes to my mind is that
> >> between run 1 and run 2 I changed the frequency of output.
> >>
> >
> > Yes, that's what the message is telling you, in case you didn't know,
> > messed up, etc.
> >
> >
> >> Still, I don't understand why I get the time series when using the
> >> tool
> >> from gromacs 4.6 (seems that it doesn't care about the timestep
> >> mismatch), but not using gromacs 5.0?
> >>
> >
> > Neither can we, since you didn't tell us what you did when you tried to
> > get
> > the time series. Here you talked about how you built your inputs.
> >
> > Mark
> >
> >
> >> Cheers,
> >> oliwia
> >>
> >>
> >> On 07.05.2015 14:59, Mark Abraham wrote:
> >> > Hi,
> >> >
> >> > Time series are what gmx distance does... see gmx distance -h, of
> >> > course.
> >> > If it's not working for you, you'll have to tell us exactly what you
> >> > tried,
> >> > what output you got, what's not suitable, etc., and check that your
> >> > input
> >> > files contain what you think they do (e.g. with gmx check)
> >> >
> >> > Mark
> >> >
> >> > On Thu, May 7, 2015 at 2:38 PM oliwias  wrote:
> >> >
> >> >> Dear All,
> >> >>
> >> >> I am trying to use the new gromacs 5.0 tools for analysis. I tried
> >> >> multiple options but I can't get gmx distance and gmx mindist to
> print
> >> >> out time series of distances. I only get the average. On the other
> >> >> hand,
> >> >> I had no problem with getting the time series with gromacs 4.6 g_dist
> >> >> and g_mindist. Don't know if it's a problem of the code or if I just
> >> >> don't know how to use the tool...
> >> >>
> >> >> I'd appreciate your tips!
> >> >> oliwia
> >> >> --
> >> >> Gromacs Users mailing list
> >> >>
> >> >> * Please search the archive at
> >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] short-range eletrostatic energy of every aminoacid

[Ullmann, Thomas]

Hi Diogo,

create an index file, either with gmx select or gmx make_ndx, and feed it to 
grompp.

Happy computing,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Diogo Martins 
de Sá [sadi...@mol.bio.br]
Sent: Monday, May 25, 2015 8:38 PM
To: gmx-users
Subject: [gmx-users] short-range eletrostatic energy of every aminoacid

Hello guys,

I'd like to do make an energy matrix of every aminoacid of a simulation
of two interacting proteins. I know enemat can assess the matrix, but
for this I have to define energygroups in .mdp files. What would be the
easiest way to achieve this?

I guess if I am going to find an easier way, I have to understand how
gromacs "finds" the energygroups I have written down in the .mdp file.
Lets say I manage to write down all the aminoacids I want in the
energygroups of the .mdp file. How would gromacs know where to look for
the atoms comprising each aminoacid? An index file, a topology file?

Thanks in advance.

Regards,
Diogo
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Re: [gmx-users] PCA of crystal structures

[Ullmann, Thomas]

Hi,

you can directly project the crystal structures onto the eigenvectors from the 
PCA with gmx anaeig.
It may be necessary to create an index file for each PDB file with an index 
group that identifies the
atoms that correspond to the vector components. Make sure that the order of 
atoms is the same in
the PDB as in the trajectories/structures used in the PCA. For multimeric 
proteins, make sure that the order of subunits is also the same.

Happy computing,
Thomas.
--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of neeru sharma 
[neeru.bioi...@gmail.com]
Sent: Monday, December 22, 2014 6:04 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] PCA of crystal structures

Dear Gromacs-users,

I have carried out MD simulations of a Protein complex starting with the
active state conformation a particular crystal structure and have carried
out PCA analysis for the same too.

Now, I want to identify the location of all the crystal structures of the
same protein (Intermediate, active, inactive, mutants etc) on the PCA plots
too but I haven't run simulations for all of these.

Can anyone suggest me the way to do so?

--Neeru Shara
C-DAC, Pune, India
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Re: [gmx-users] All atom MD Simulation

[Ullmann, Thomas]

>> Can we analyse catalytic mechanism of an enzyme using the classical all
>> atom MD simulation.
>
>No.

I would say, that is a bit too pessimistic and unnecessarily demotivating. You 
can not directly simulate the catalytic reaction without employing  a quantum 
chemical treatment (or a reactive force field) for the catalytic site and the 
reacting compounds, but even without that, just with classical MD, you can 
still learn a lot about the enzymatic mechanism, e.g., about the binding of a 
substrate, the stabilization of reaction intermediates with respect to educt(s) 
and product(s)  in the catalytic site relative to the same reaction in 
solution, the release of a product(s) etc. A literature research will turn up 
innumerable examples.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Wednesday, September 03, 2014 1:42 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] All atom MD Simulation

On 9/3/14, 7:40 AM, Anitha wrote:
> Can we analyse catalytic mechanism of an enzyme using the classical all
> atom MD simulation.
>

No.

-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] Constant pH simulations

[Ullmann, Thomas]

Hi,

Not yet, but we are working on it.

Best,
Thomas.


--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Douglas 
Grahame [dgrah...@uoguelph.ca]
Sent: Sunday, July 06, 2014 6:48 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Constant pH simulations

Hi everyone, I was wondering if anyone has any experience or knows of a
tutorial site that I could look at for performing constant pH simulations.
I've checked out the info on the gromacs.org web site and a few others such
as (http://www.mpibpc.mpg.de/247796/usage) but I was wondering if there is
anything more up to date than what I've found so far. Cheers,



-Douglas Grahame

BSc. MSc. PhD. Candidate

dgrah...@uoguelph.ca





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