Re: [gmx-users] CMAP format on GROMACS

[Justin Lemkul]

On 1/8/20 10:25 AM, Marcelo Depólo wrote:

Thanks for your input, Justin. Helpful as always.


I am assuming the array is formatted to vary phi as a function of psi
i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and
again but for phi = -165.

I am also assuming that, since it is a 24x24 matrix, values will start in
phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix
would lead to end in phi=180,psi=180, but since they -180 and 180 are
equivalent, maybe GROMACS already do this workaround?


+/- 180 are understood to be equivalent.


The last question: are those values in kJ/mol?


Yes. GROMACS always uses SI units.

-Justin

--
==

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

Virginia Tech Department of Biochemistry
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Re: [gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

[Justin Lemkul]

On 1/8/20 11:12 AM, Matthew Fisher wrote:

Dear all,

I'm simulating the effect of amino acid mutations on tertiary structure and, 
for benchmarking purposes, I want to compare the RMS of my in silico variant 
trajectories (prepared from the WT structure) to their cystallographic 
structures.

In the gmx rms command, when I select the structure for the -s flag, should I 
use the pdb file from the RCSB, or alternatively should I take the crystal 
structure, parametise it using pdb2gmx and then take the pre-minimisation .tpr 
file? Alternatively is there something else I should be doing? Any advice would 
be appreciated.


The latter is the best approach as it will allow for proper 
mass-weighting in the RMSD calculation.


-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] Vibrational spectra of amide I using gromacs

[André Farias de Moura]

Dear Mijiddorj,

It is a matter of taste, but I like to use xmgrace for that kind of
analysis.

The GROMACS tool gmx analyze can do that for you:
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html

Andre

On Wed, Jan 8, 2020 at 9:18 PM Mijiddorj B  wrote:

> Dear Andre
>
> Thank you very much for your quick response.
> I am very new for this type of analysis, and I would like to ask further. I
> am sorry for that. Is there any good software?
> If you have any experience, please suggest me some useful software for the
> time series correlation and the Fourier transformation.
>
> Best regards,
>
> Mijiddorj
>
> Should be doable using any standard spreadsheet:
> >
> > (1) save the bond lengths along the simulation for the bond of interest
> >
> > (2) compute the time correlation function for these bond lengths (the
> > autocorrelation function for this time series)
> >
> > (3) compute the Fourier transform of the time correlation function
> >
> > Andre
> >
> > On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B 
> wrote:
> >
> > > Dear gmx users,
> > >
> > > Hello, I would like to ask vibrational spectra of amide of specific
> > > amino acids. Is it possible to analyze from classic MD calculations of
> > > gromacs?
> > > Or
> > >
> > > Is there any software that is compatible with gmx trajectories  to
> > > calculate the spectra?
> > >
> > > Best regards,
> > >
> > > Mijiddorj
> > > --
> > > 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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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> > --
> > _
> >
> > Prof. Dr. Andr? Farias de Moura
> > Department of Chemistry
> > Federal University of S?o Carlos
> > S?o 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] Vibrational spectra of amide I using gromacs

[Mijiddorj B]

Dear Andre

Thank you very much for your quick response.
I am very new for this type of analysis, and I would like to ask further. I
am sorry for that. Is there any good software?
If you have any experience, please suggest me some useful software for the
time series correlation and the Fourier transformation.

Best regards,

Mijiddorj

Should be doable using any standard spreadsheet:
>
> (1) save the bond lengths along the simulation for the bond of interest
>
> (2) compute the time correlation function for these bond lengths (the
> autocorrelation function for this time series)
>
> (3) compute the Fourier transform of the time correlation function
>
> Andre
>
> On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B  wrote:
>
> > Dear gmx users,
> >
> > Hello, I would like to ask vibrational spectra of amide of specific
> > amino acids. Is it possible to analyze from classic MD calculations of
> > gromacs?
> > Or
> >
> > Is there any software that is compatible with gmx trajectories  to
> > calculate the spectra?
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > 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.
> >
>
>
> --
> _
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> --
>
>
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 18

[Mijiddorj B]

Dear Andre

Thank you very much for your quick response.
I am very new for this type of analysis, and I would like to ask further. I
am sorry for that. Is there any good software?
If you have any experience, please suggest me some useful software for the
time series correlation and the Fourier transformation.

Best regards,

Mijiddorj

>
> Should be doable using any standard spreadsheet:
>
> (1) save the bond lengths along the simulation for the bond of interest
>
> (2) compute the time correlation function for these bond lengths (the
> autocorrelation function for this time series)
>
> (3) compute the Fourier transform of the time correlation function
>
> Andre
>
> On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B  wrote:
>
> > Dear gmx users,
> >
> > Hello, I would like to ask vibrational spectra of amide of specific
> > amino acids. Is it possible to analyze from classic MD calculations of
> > gromacs?
> > Or
> >
> > Is there any software that is compatible with gmx trajectories  to
> > calculate the spectra?
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > 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.
> >
>
>
> --
> _
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
>
>
> --
>
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Re: [gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

[Bratin Kumar Das]

Use the .tpr file generated by grompp module

On Wed 8 Jan, 2020, 9:43 PM Matthew Fisher, 
wrote:

> Dear all,
>
> I'm simulating the effect of amino acid mutations on tertiary structure
> and, for benchmarking purposes, I want to compare the RMS of my in silico
> variant trajectories (prepared from the WT structure) to their
> cystallographic structures.
>
> In the gmx rms command, when I select the structure for the -s flag,
> should I use the pdb file from the RCSB, or alternatively should I take the
> crystal structure, parametise it using pdb2gmx and then take the
> pre-minimisation .tpr file? Alternatively is there something else I should
> be doing? Any advice would be appreciated.
>
> Best wishes,
> Matthew
>
>
> --
> Gromacs Users mailing list
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[gmx-users] Comparing the RMSD of an in silico variant to a crystal structure.

[Matthew Fisher]

Dear all,

I'm simulating the effect of amino acid mutations on tertiary structure and, 
for benchmarking purposes, I want to compare the RMS of my in silico variant 
trajectories (prepared from the WT structure) to their cystallographic 
structures.

In the gmx rms command, when I select the structure for the -s flag, should I 
use the pdb file from the RCSB, or alternatively should I take the crystal 
structure, parametise it using pdb2gmx and then take the pre-minimisation .tpr 
file? Alternatively is there something else I should be doing? Any advice would 
be appreciated.

Best wishes,
Matthew


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[gmx-users] is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version?

[Jimmy Chen]

Hi,

is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version
on NVidia GPU?
or just work only in single-node with threadMPI via Nvidia GPU direct?

Thanks,
Jimmy
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Re: [gmx-users] cant compute msd

[Devargya Chakraborty]

After removing the -mol command it worked fine.

On Wed, Jan 8, 2020, 3:53 PM Christian Blau  wrote:

> Hi Devargya,
>
>
> I believe it's the mixture of -mol and -o options at the same time that
> leads to the unexpected behaviour - there can
> only be one .xvg output for this tool and we'll see to having it fixed.
>
> Do you get any diff_mol.xvg files instead?
>
>
> The documentation states that
>
> "If -mol is set, gmx msd plots the MSD for individual molecules (including
> making molecules whole across periodic boundaries): for each individual
> molecule a diffusion constant is computed for its center of mass. The
> chosen
> index group will be split into molecules."
>
>
> Best,
>
> Christian
>
>
> On 2020-01-08 11:12, Devargya Chakraborty wrote:
> > hi, when i am using the command
> >   gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg
> >
> > after that choosing a group the following line is coming.
> > Select a group to calculate mean squared displacement for:
> > Group 0 ( System) has  5616 elements
> > Group 1 (  Other) has  5616 elements
> > Group 2 ( c2) has  2376 elements
> > Group 3 (   ntf2) has  3240 elements
> > Group 4 (  N) has   216 elements
> > Group 5 (  N) has   216 elements
> > Select a group: 3
> > Selected 3: 'ntf2'
> > Split group of 3240 atoms into 216 molecules
> > Reading frame5000 time 2.000   Killed
> >
> > and i cant get the msd file any suggestion regarding this??
> >
> > thank you
> --
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Re: [gmx-users] CMAP format on GROMACS

[Marcelo Depólo]

Thanks for your input, Justin. Helpful as always.


I am assuming the array is formatted to vary phi as a function of psi
i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and
again but for phi = -165.

I am also assuming that, since it is a 24x24 matrix, values will start in
phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix
would lead to end in phi=180,psi=180, but since they -180 and 180 are
equivalent, maybe GROMACS already do this workaround?

The last question: are those values in kJ/mol?

Cheers!
--
Marcelo


> The \ are line continuation characters, so GROMACS is reading a 24x24
> matrix in a single array of values.
>
> The values are written for all values of phi at a given value of psi,
> i.e. writing each row of the matrix, starting from phi = -180, psi =
> -180 until phi = 180, psi = 180.
>
> -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
>
> ==
>
>
>
> --
>
> Message: 4
> Date: Tue, 7 Jan 2020 11:40:30 +0900
> From: ??? 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] The maxwarn fatal errors
> Message-ID: <4b64c77f-360f-44ca-b051-11df14d7f...@gmail.com>
> Content-Type: text/plain;   charset=us-ascii
>
> Dear everyone, Happy New year!
> I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
>   gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
>
> I have met two warnings and they occured fatal error.:
>   Fatal error:
>   Too many warnings (2).
>If you are sure all warnings are harmless, use the -maxwarn option.
>
> And the waring is:
>  WARNING 1 [file topol.top, line 56]:
>   The GROMOS force fields have been parametrized with a physically
>   incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>   used with a single-range cut-off (or a correct Trotter
>   multiple-time-stepping scheme), physical properties, such as the density,
>   might differ from the intended values. Since there are researchers
>   actively working on validating GROMOS with modern integrators we have not
>   yet removed the GROMOS force fields, but you should be aware of these
>   issues and check if molecules in your system are affected before
>   proceeding. Further information is available at
>   https://redmine.gromacs.org/issues/2884 , and a longer explanation of
> our
>   decision to remove physically incorrect algorithms can be found at
>   https://doi.org/10.26434/chemrxiv.11474583.v1 .
>
>
> WARNING 2 [file md_umbrella.mdp]:
>   With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
>   should be at least twice as large as tau-t (1) to avoid resonances
>
> I solved this problem with using -maxwarn option but I am wondering
> whether thses warning is passed over.
> What do you think what I happend? dears. Any idea on what caused this
> problem?
>
> --
>
> Message: 5
> Date: Mon, 6 Jan 2020 21:41:28 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] The maxwarn fatal errors
> Message-ID: <89785204-b49e-4f0c-3da9-10abd0b13...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/6/20 9:40 PM, ??? wrote:
> > Dear everyone, Happy New year!
> > I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
> >gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
> >
> > I have met two warnings and they occured fatal error.:
> >Fatal error:
> >Too many warnings (2).
> > If you are sure all warnings are harmless, use the -maxwarn option.
> >
> > And the waring is:
> >   WARNING 1 [file topol.top, line 56]:
> >The GROMOS force fields have been parametrized with a physically
> >incorrect multiple-time-stepping scheme for a twin-range cut-off. When
> >used with a single-range cut-off (or a correct Trotter
> >multiple-time-stepping scheme), physical properties, such as the
> density,
> >might differ from the intended values. Since there are researchers
> >actively working on validating GROMOS with modern integrators we have
> not
> >yet removed the GROMOS force fields, but you should be aware of these
> >issues and check if molecules in your system are affected before
> >proceeding. Further information is available at
> >https://redmine.gromacs.org/issues/2884 , and a longer explanation
> of our
> >decision to remove physically incorrect algorithms can be found at
> >

Re: [gmx-users] Vibrational spectra of amide I using gromacs

[André Farias de Moura]

Should be doable using any standard spreadsheet:

(1) save the bond lengths along the simulation for the bond of interest

(2) compute the time correlation function for these bond lengths (the
autocorrelation function for this time series)

(3) compute the Fourier transform of the time correlation function

Andre

On Wed, Jan 8, 2020 at 11:37 AM Mijiddorj B  wrote:

> Dear gmx users,
>
> Hello, I would like to ask vibrational spectra of amide of specific
> amino acids. Is it possible to analyze from classic MD calculations of
> gromacs?
> Or
>
> Is there any software that is compatible with gmx trajectories  to
> calculate the spectra?
>
> Best regards,
>
> Mijiddorj
> --
> 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.
>


-- 
_

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] Position restrains calculation of virial

[Alessandra Villa]

Hi Johannes,

On Wed, Jan 8, 2020 at 11:29 AM Johannes Hermann 
wrote:

> Dear all,
>
> how is the virial computed when position restraints are applied? Are
> forces due to position restrains included or excluded?
>
>
Yes the the forces due to position restrains are included.

But I think that this does not necessary imply  that  the pressure is well
defined in NVT with position restrains
I recall that you had such a question a while ago
"Is the pressure well defined when I use position restrains
in NVT?"

Best regards
Alessandra

> Thanks!
>
> All the best
>
> Johannes
>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: johannes.herm...@tum.de
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[gmx-users] Vibrational spectra of amide I using gromacs

[Mijiddorj B]

Dear gmx users,

Hello, I would like to ask vibrational spectra of amide of specific
amino acids. Is it possible to analyze from classic MD calculations of
gromacs?
Or

Is there any software that is compatible with gmx trajectories  to
calculate the spectra?

Best regards,

Mijiddorj
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Re: [gmx-users] system has non zero net charge

[Justin Lemkul]

On 1/8/20 6:01 AM, Yogesh Sharma wrote:

Greetings,
I am performing membrane protein simulation in the presence of a
biomolecule. topology for the molecule was downloaded from ATB server.
After simulation run, I found unexpected behviour of the added
biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
residues. ligand didnt seperate through out simulation once bound, which is
highly unexpected at neutral pH.


Why is that unexpected? Your ligand is Si(OH)4 and likely participates 
in hydrogen-bonding interactions very easily with charged groups.



I was getting these two notes during solvation.

Generated 1062 of the 3486 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'POPC'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'U1NL'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...

NOTE 1 [file topol2.top, line 18875]:
   System has non-zero total charge: -1.02
   Total charge should normally be an integer.


The discrepancy between your value and -1 is simply due to rounding. The 
larger issue is you have a membrane system with a net charge. If you 
allow PME to apply a neutralizing background plasma to this system (i.e. 
you don't use counterions), you will get very severe artifacts.



Is it possible this -1 charge is producing artifact. I have addded 20
molecules of same ligand in my system and 6 of them are binding to negative
charged residues.
I checked total charge on ligand.itp file, its zero. then i checked line
18875 in topol2.top its SOL which is highly unlikely to have any charge.
U1NL 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
 1  HS141U1NL H4 10.480   1.0080
 2 OEOpt1U1NL O42   -0.814  15.9994
 3SI 1U1NL Si 31.336   28.0800
 4 OEOpt1U1NL O14   -0.814  15.9994
 5  HS14 1U1NL H1 50.480   1.0080
 6 OEOpt1U1NL O26   -0.814  15.9994
 7  HS14 1U1NL H3 70.480   1.0080
 8 OEOpt1U1NL O38   -0.814  15.9994
 9  HS141U1NL H2 90.480   1.0080
; total charge of the molecule:  -0.000

How can i check what molecule is throwing this negative -1 charge to my
system?


POPC is uncharged, water is uncharged, your ligand is uncharged, so the 
charge must be coming from...? :)


-Justin

--
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Lab: 303 Engel Hall

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Justin Lemkul]

On 1/8/20 4:49 AM, Christian Blau wrote:

Hi Navnett,


gmx select will be your friend.


At the bottom of

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html 



you'll find some example commands. Something along the lines of

  gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much 
worth the effort reading through that documentation.




It's also simple in make_ndx:

3 & r 150-210

Either way works. Whatever you find easier to use.

-Justin

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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] Simulated Annealing command line

[Justin Lemkul]

On 1/7/20 6:35 PM, Neena Susan Eappen wrote:

Hi Justin,

Thank you for your answer. I haven't written scripts before, so I was wondering 
is there a sample script I can see for looping in gromacs.


What you're trying to do is similar to the logic in 
http://www.mdtutorials.com/gmx/membrane_protein/Files/run_inflategro.sh


-Justin

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==

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Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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[gmx-users] how to set system for absolute free enegy calculation of ligand in protein

[Sadaf Rani]

Dear Gromacs users
I need your suggestions regarding the calculation of free energy of binding
in of ligand protein-ligand complex in setting up the system.
I am performing binding free energy calculation following alchemical free
energy path. I added a single molecule type in topology for both protein
and ligand in order to add distance restraints between ligand and protein
atoms however for decoupling ligand from protein I need a separate molecule
type for the ligand.
How should I set the system to avoid this problem?

Thanks in advance.

Sadaf
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Re: [gmx-users] system has non zero net charge

[Gudrun Gygli]

Hi Yogesh,

this happens to me as well sometimes, there are several options:

- your protein is not neutral (my best practice is to you use pdb2gmx 
interactively and set the charges for all amino acids manually following 
pkA predictions by e.g. Propka - then you will immediately know if the 
protien has a charge from the output)


- one of your itp files (I guess POPC and U1NL are from ATB) has a 
non-zero charge - make sure to show 10 decimal points when you calculate 
the total charge of all the atoms in the ligands, it happens sometimes 
that these do NOT add up to a completely neutral value, and rounding 
errors will occur and mess up the total charge of your system - 
especially if you add 20 identical molecules It is always a good 
idea to carefully check the parameters obtained from ATB or another 
server - mistakes happen!


- if the charge persists, you must neutralise the system using genion: 
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genion.html


Best of luck

Gudrun


Am 08.01.2020 um 12:01 schrieb Yogesh Sharma:

Greetings,
I am performing membrane protein simulation in the presence of a
biomolecule. topology for the molecule was downloaded from ATB server.
After simulation run, I found unexpected behviour of the added
biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
residues. ligand didnt seperate through out simulation once bound, which is
highly unexpected at neutral pH.

I was getting these two notes during solvation.

Generated 1062 of the 3486 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'POPC'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'U1NL'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...

NOTE 1 [file topol2.top, line 18875]:
   System has non-zero total charge: -1.02
   Total charge should normally be an integer.

Is it possible this -1 charge is producing artifact. I have addded 20
molecules of same ligand in my system and 6 of them are binding to negative
charged residues.
I checked total charge on ligand.itp file, its zero. then i checked line
18875 in topol2.top its SOL which is highly unlikely to have any charge.

U1NL 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
 1  HS141U1NL H4 10.480   1.0080
 2 OEOpt1U1NL O42   -0.814  15.9994
 3SI 1U1NL Si 31.336   28.0800
 4 OEOpt1U1NL O14   -0.814  15.9994
 5  HS14 1U1NL H1 50.480   1.0080
 6 OEOpt1U1NL O26   -0.814  15.9994
 7  HS14 1U1NL H3 70.480   1.0080
 8 OEOpt1U1NL O38   -0.814  15.9994
 9  HS141U1NL H2 90.480   1.0080
; total charge of the molecule:  -0.000

How can i check what molecule is throwing this negative -1 charge to my
system?
Thankyou in advance for your valuable time.

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[gmx-users] system has non zero net charge

[Yogesh Sharma]

Greetings,
I am performing membrane protein simulation in the presence of a
biomolecule. topology for the molecule was downloaded from ATB server.
After simulation run, I found unexpected behviour of the added
biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
residues. ligand didnt seperate through out simulation once bound, which is
highly unexpected at neutral pH.

I was getting these two notes during solvation.

Generated 1062 of the 3486 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'POPC'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'U1NL'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...

NOTE 1 [file topol2.top, line 18875]:
  System has non-zero total charge: -1.02
  Total charge should normally be an integer.

Is it possible this -1 charge is producing artifact. I have addded 20
molecules of same ligand in my system and 6 of them are binding to negative
charged residues.
I checked total charge on ligand.itp file, its zero. then i checked line
18875 in topol2.top its SOL which is highly unlikely to have any charge.

U1NL 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
1  HS141U1NL H4 10.480   1.0080
2 OEOpt1U1NL O42   -0.814  15.9994
3SI 1U1NL Si 31.336   28.0800
4 OEOpt1U1NL O14   -0.814  15.9994
5  HS14 1U1NL H1 50.480   1.0080
6 OEOpt1U1NL O26   -0.814  15.9994
7  HS14 1U1NL H3 70.480   1.0080
8 OEOpt1U1NL O38   -0.814  15.9994
9  HS141U1NL H2 90.480   1.0080
; total charge of the molecule:  -0.000

How can i check what molecule is throwing this negative -1 charge to my
system?
Thankyou in advance for your valuable time.
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[gmx-users] Position restrains calculation of virial

[Johannes Hermann]

Dear all,

how is the virial computed when position restraints are applied? Are 
forces due to position restrains included or excluded?


Thanks!

All the best

Johannes

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*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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Tel: +49 8928915730
Fax: +49 8928915714

Email: johannes.herm...@tum.de
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Re: [gmx-users] cant compute msd

[Christian Blau]

Hi Devargya,


I believe it's the mixture of -mol and -o options at the same time that leads to the unexpected behaviour - there can 
only be one .xvg output for this tool and we'll see to having it fixed.


Do you get any diff_mol.xvg files instead?


The documentation states that

"If -mol is set, gmx msd plots the MSD for individual molecules (including
making molecules whole across periodic boundaries): for each individual
molecule a diffusion constant is computed for its center of mass. The chosen
index group will be split into molecules."


Best,

Christian


On 2020-01-08 11:12, Devargya Chakraborty wrote:

hi, when i am using the command
  gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg

after that choosing a group the following line is coming.
Select a group to calculate mean squared displacement for:
Group 0 ( System) has  5616 elements
Group 1 (  Other) has  5616 elements
Group 2 ( c2) has  2376 elements
Group 3 (   ntf2) has  3240 elements
Group 4 (  N) has   216 elements
Group 5 (  N) has   216 elements
Select a group: 3
Selected 3: 'ntf2'
Split group of 3240 atoms into 216 molecules
Reading frame5000 time 2.000   Killed

and i cant get the msd file any suggestion regarding this??

thank you

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[gmx-users] cant compute msd

[Devargya Chakraborty]

hi, when i am using the command
 gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg

after that choosing a group the following line is coming.
Select a group to calculate mean squared displacement for:
Group 0 ( System) has  5616 elements
Group 1 (  Other) has  5616 elements
Group 2 ( c2) has  2376 elements
Group 3 (   ntf2) has  3240 elements
Group 4 (  N) has   216 elements
Group 5 (  N) has   216 elements
Select a group: 3
Selected 3: 'ntf2'
Split group of 3240 atoms into 216 molecules
Reading frame5000 time 2.000   Killed

and i cant get the msd file any suggestion regarding this??

thank you
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Re: [gmx-users] How to rotate the molecule in box

[Christian Blau]

Hi Yeping,


The center of rotation is (0,0,0) for the rotate command, which is the lower left front corner of your box, and not the 
box center. That's why the molecule moves out of the box when rotating.


One (of conceivable more ways) to perform the rotation, is to use -center (0,0,0) to create a new structure, centered on 
the origin, then perform the rotation, and then shift the molecule back into the box center with -center only.



Best,

Christian


On 2019-12-30 14:44, sunyeping wrote:

Dear all,

By using the editconf command, we can build a box for the protein molecule, for 
example:

  gmx editconf -f complex.gro -o newbox.gro -c -d 1.2 -bt cubic

but how to rotate the molecule in the box? I tried to use "-rotate" option of 
the editconf command to do so, but I found part of the molecule goes out the pbc box 
after rotation. Please refer to the image at the following link:

https://drive.google.com/file/d/1P_yTeRSkHpeUTXSUZMlTw2AHZ17s0htv/view?usp=sharing

The molecule was orignally at position 1. I wanted to rotate the molecule 
around x and y axes by 45 degrees. After I ran the following command:

 gmx editconf -f newbox.gro -rotate 45 45 0 -bt o -o newbpx_1.gro

The molecule went to position 2. You can see part of the molecule are now out 
of the box.

Do you know how to rotate the molecule but keep it within the box?

Thank you in advance.

Yeping

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thank You, Sir!

On Wed, Jan 8, 2020 at 3:19 PM Christian Blau  wrote:

> Hi Navnett,
>
>
> gmx select will be your friend.
>
>
> At the bottom of
>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
>
> you'll find some example commands. Something along the lines of
>
>gmx select -select 'name CA and resid > 149 and resid < 211'
>
> should work.
>
>
> It's a very powerful syntax and I figured for me it was very much worth
> the effort reading through that documentation.
>
>
> Best,
>
> Chrsitian
>
> On 2020-01-08 10:42, Navneet Kumar wrote:
> > Sorry, it should be 150-200 residues.
> >
> > On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar 
> wrote:
> >
> >> Hello Everyone!
> >>
> >>
> >> How to create an index group for Backbone/C-alpha for a specific set of
> >> residues from protein? (Say Protein with 200 amino acid; want to create
> an
> >> index group for the backbone of residues 150-210).
> >> Regards
> >> Navneet Kumar
> >>
> >>
> >>
> >>
> >>
> >>
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 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Christian Blau]

Hi Navnett,


gmx select will be your friend.


At the bottom of

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html

you'll find some example commands. Something along the lines of

  gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much worth the 
effort reading through that documentation.


Best,

Chrsitian

On 2020-01-08 10:42, Navneet Kumar wrote:

Sorry, it should be 150-200 residues.

On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar  wrote:


Hello Everyone!


How to create an index group for Backbone/C-alpha for a specific set of
residues from protein? (Say Protein with 200 amino acid; want to create an
index group for the backbone of residues 150-210).
Regards
Navneet Kumar







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Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Sorry, it should be 150-200 residues.

On Wed, Jan 8, 2020 at 3:09 PM Navneet Kumar  wrote:

> Hello Everyone!
>
>
> How to create an index group for Backbone/C-alpha for a specific set of
> residues from protein? (Say Protein with 200 amino acid; want to create an
> index group for the backbone of residues 150-210).
> Regards
> Navneet Kumar
>
>
>
>
>
>

-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

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[gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Hello Everyone!


How to create an index group for Backbone/C-alpha for a specific set of
residues from protein? (Say Protein with 200 amino acid; want to create an
index group for the backbone of residues 150-210).
Regards
Navneet Kumar
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Re: [gmx-users] Make index command in gromacs

[Christian Blau]

Hi Shan,


gmx select gives you many more options to do complex arithmetic with selections 
that might help you here.


You can try using

gmx select -select "SELECTION STING"

you'll find lots of selection string examples at the bottom in here:

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html



Best,

Christian


On 2020-01-07 23:33, Shan Jayasinghe wrote:

Dear Gromacs Users,

In my simulations, I have different sizes of water droplets.  I need
indexes of water molecules in each droplet separately. I am trying to make
the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
help regarding this matter.

Thank you.

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Re: [gmx-users] Make index command in gromacs

[Alessandra Villa]

Hi,

Maybe you could  use gmx select to generate your index file
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html?highlight=select

Best regards
Alessandra

On Tue, Jan 7, 2020 at 11:39 PM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Gromacs Users,
>
> In my simulations, I have different sizes of water droplets.  I need
> indexes of water molecules in each droplet separately. I am trying to make
> the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
> help regarding this matter.
>
> Thank you.
> --
> Best Regards
> Shan Jayasinghe
> --
> 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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