Re: [gmx-users] Energy from a subgroup of molecules

[Justin Lemkul]

On 4/11/19 5:39 PM, paul buscemi wrote:

Thank you for the response, Mark.

I do use the rerun tactic, and this is not too bad for a small number of 
molecules

  but is there a way to include the index information within the mdrun (rerun ) 
… something like

gmx mdrun  -s adsorb.ener_gp.tpr  -rerun adsorb,npt.trr   - n use_only.ndx  ?

or use the  indices within the grompp command ?



The only solution is what Mark proposed - create a .tpr file with the 
required energygrps and use mdrun -rerun. mdrun does not accept an index 
file.


-Justin


Paul


On Apr 11, 2019, at 1:48 AM, Mark Abraham  wrote:

Hi,

You can't do that with gmx energy, as you need mdrun to understand the new
grouping. But making a new .tpr with the energy groups so defined permits
you to use gmx mdrun -rerun for such a single point energy evaluation.

Mark

On Wed., 10 Apr. 2019, 22:24 p buscemi,  wrote:


Dear Users,
I've performed an adsorption experiment in which a fraction of molecules
in solution adsorb to a surface. I can extract the index of those adsorbed,
and I can obtain the total interaction ( LJ ) of the energy group with the
surface.
I can estimate the average interaction of the adsorbed molecules by
dividing the total energy by the number of molecules within a certain
distance ( the index number )
How might I use gmx energy to recalculate the interaction using the
original surface but only the adsorbed molecules specified in the index
file... something like
"gmx energy -f starting.gro -n index.ndx"

A single point calculation would be quite satisfactory.
thanks
Paul
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==

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Lab: 303 Engel Hall

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Re: [gmx-users] Energy from a subgroup of molecules

[paul buscemi]

Thank you for the response, Mark.

I do use the rerun tactic, and this is not too bad for a small number of 
molecules

 but is there a way to include the index information within the mdrun (rerun ) 
… something like 

gmx mdrun  -s adsorb.ener_gp.tpr  -rerun adsorb,npt.trr   - n use_only.ndx  ?

or use the  indices within the grompp command ?


Paul

> On Apr 11, 2019, at 1:48 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> You can't do that with gmx energy, as you need mdrun to understand the new
> grouping. But making a new .tpr with the energy groups so defined permits
> you to use gmx mdrun -rerun for such a single point energy evaluation.
> 
> Mark
> 
> On Wed., 10 Apr. 2019, 22:24 p buscemi,  wrote:
> 
>> 
>> Dear Users,
>> I've performed an adsorption experiment in which a fraction of molecules
>> in solution adsorb to a surface. I can extract the index of those adsorbed,
>> and I can obtain the total interaction ( LJ ) of the energy group with the
>> surface.
>> I can estimate the average interaction of the adsorbed molecules by
>> dividing the total energy by the number of molecules within a certain
>> distance ( the index number )
>> How might I use gmx energy to recalculate the interaction using the
>> original surface but only the adsorbed molecules specified in the index
>> file... something like
>> "gmx energy -f starting.gro -n index.ndx"
>> 
>> A single point calculation would be quite satisfactory.
>> thanks
>> Paul
>> --
>> 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.
>> 
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Re: [gmx-users] gromacs instillation

[Ali Ahmed]

Yes I'm using the quick and dirty Installation

On Thu, Apr 11, 2019 at 12:55 PM RAHUL SURESH 
wrote:

> Are you following the quick and dirty Installation or modify your
> compilation?
>
> On Thu 11 Apr, 2019, 11:20 PM RAHUL SURESH, 
> wrote:
>
> >
> >
> > On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,  wrote:
> >
> >> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes,
> each
> >> terminal I run source /usr/local/gromacs/bin/GMXRC to strat using
> gromacs.
> >> I kind of confused which one I should modify
> >>
> >
> > If that is your executable directory, then there is nothing to modify.
> > What error actually you get?
> >
> > Please try the command gmx_mpi after source command. (A wild guess)
> >
> > Thank you
> >
> >
> >
> >>
> >> On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:
> >>
> >> > when you open a new terminal you need to run " source" again, but you
> >> > probably know this by now
> >> > or
> >> > add the path to your /etc/.profile to make the change permanent
> >> >
> >> > Sent from Mailspring (
> >> >
> >>
> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn
> >> ),
> >> > the best free email app for work
> >> > On Apr 11 2019, at 1:45 am, Mark Abraham 
> >> wrote:
> >> > > Hi,
> >> > >
> >> > > Each shell you open needs to be told how to find GROMACS, per
> >> > >
> >> >
> >>
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
> >> > >
> >> > > Mark
> >> > > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed, 
> wrote:
> >> > > > Hello GMX users
> >> > > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
> >> > well.
> >> > > > I run: source /usr/local/gromacs/bin/GMXRC and checked the
> version,
> >> it
> >> > was
> >> > > > 2019.1.
> >> > > > When I open a new terminal and hit gmx, it says gromacs is
> currently
> >> > not
> >> > > > installed. You can install it by typing: sudo apt install gromacs.
> >> > When I
> >> > > > did it, the version became 5.1.2.
> >> > > >
> >> > > > Any idea how to solve it!
> >> > > > Thank you
> >> > > > Ali
> >> > > > --
> >> > > > 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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> >> > 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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> >> >
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> >> > posting!
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> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
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> >>
> >
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Re: [gmx-users] Different versions of gromacs

[Bratin Kumar Das]

Thnxx sir

On Thu 11 Apr, 2019, 8:46 PM Justin Lemkul 
> More specifically, versions within a release series that only differ by
> patch number (e.g. 2016.x, 2018.x, etc) are designed to be compatible. I
> would not personally do different processes in the same project with
> different major versions.
>
> -Justin
>
> On 4/10/19 10:56 PM, Bratin Kumar Das wrote:
> > Thanks
> >
> > On Wed 10 Apr, 2019, 4:52 PM RAHUL SURESH  wrote:
> >
> >> It won't work in lower version than 2016. I don't think it will have any
> >> problem with higher version and influence of the mdrun is not altered I
> >> guess as it is a factor of your mdp settings for higher versions
> >>
> >> On Wed 10 Apr, 2019, 3:41 PM Bratin Kumar Das, <
> >> 177cy500.bra...@nitk.edu.in>
> >> wrote:
> >>
> >>> Hi
> >>>  Can I run equilibration simulation in one version (ex
> gromacs2016.5)
> >>> and production simulation in other version. Do the version have some
> >>> influence in simulation.
> >>> --
> >>> Gromacs Users mailing list
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> >>> posting!
> >>>
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> >>
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> >>
>
> --
> ==
>
> 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] gromacs instillation

[RAHUL SURESH]

Are you following the quick and dirty Installation or modify your
compilation?

On Thu 11 Apr, 2019, 11:20 PM RAHUL SURESH,  wrote:

>
>
> On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,  wrote:
>
>> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each
>> terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs.
>> I kind of confused which one I should modify
>>
>
> If that is your executable directory, then there is nothing to modify.
> What error actually you get?
>
> Please try the command gmx_mpi after source command. (A wild guess)
>
> Thank you
>
>
>
>>
>> On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:
>>
>> > when you open a new terminal you need to run " source" again, but you
>> > probably know this by now
>> > or
>> > add the path to your /etc/.profile to make the change permanent
>> >
>> > Sent from Mailspring (
>> >
>> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn
>> ),
>> > the best free email app for work
>> > On Apr 11 2019, at 1:45 am, Mark Abraham 
>> wrote:
>> > > Hi,
>> > >
>> > > Each shell you open needs to be told how to find GROMACS, per
>> > >
>> >
>> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
>> > >
>> > > Mark
>> > > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
>> > > > Hello GMX users
>> > > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
>> > well.
>> > > > I run: source /usr/local/gromacs/bin/GMXRC and checked the version,
>> it
>> > was
>> > > > 2019.1.
>> > > > When I open a new terminal and hit gmx, it says gromacs is currently
>> > not
>> > > > installed. You can install it by typing: sudo apt install gromacs.
>> > When I
>> > > > did it, the version became 5.1.2.
>> > > >
>> > > > Any idea how to solve it!
>> > > > Thank you
>> > > > Ali
>> > > > --
>> > > > 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.
>> > >
>> >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
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>> > 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.
>> >
>> --
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>>
>> * 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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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] gromacs instillation

[RAHUL SURESH]

On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,  wrote:

> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each
> terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs.
> I kind of confused which one I should modify
>

If that is your executable directory, then there is nothing to modify. What
error actually you get?

Please try the command gmx_mpi after source command. (A wild guess)

Thank you



>
> On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:
>
> > when you open a new terminal you need to run " source" again, but you
> > probably know this by now
> > or
> > add the path to your /etc/.profile to make the change permanent
> >
> > Sent from Mailspring (
> >
> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn
> ),
> > the best free email app for work
> > On Apr 11 2019, at 1:45 am, Mark Abraham 
> wrote:
> > > Hi,
> > >
> > > Each shell you open needs to be told how to find GROMACS, per
> > >
> >
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
> > >
> > > Mark
> > > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
> > > > Hello GMX users
> > > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
> > well.
> > > > I run: source /usr/local/gromacs/bin/GMXRC and checked the version,
> it
> > was
> > > > 2019.1.
> > > > When I open a new terminal and hit gmx, it says gromacs is currently
> > not
> > > > installed. You can install it by typing: sudo apt install gromacs.
> > When I
> > > > did it, the version became 5.1.2.
> > > >
> > > > Any idea how to solve it!
> > > > Thank you
> > > > Ali
> > > > --
> > > > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> > --
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> >
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Re: [gmx-users] gromacs instillation

[Ali Ahmed]

I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each
terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs.
I kind of confused which one I should modify


On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:

> when you open a new terminal you need to run " source" again, but you
> probably know this by now
> or
> add the path to your /etc/.profile to make the change permanent
>
> Sent from Mailspring (
> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn),
> the best free email app for work
> On Apr 11 2019, at 1:45 am, Mark Abraham  wrote:
> > Hi,
> >
> > Each shell you open needs to be told how to find GROMACS, per
> >
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
> >
> > Mark
> > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
> > > Hello GMX users
> > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
> well.
> > > I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it
> was
> > > 2019.1.
> > > When I open a new terminal and hit gmx, it says gromacs is currently
> not
> > > installed. You can install it by typing: sudo apt install gromacs.
> When I
> > > did it, the version became 5.1.2.
> > >
> > > Any idea how to solve it!
> > > Thank you
> > > Ali
> > > --
> > > 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] Different versions of gromacs

[Justin Lemkul]

More specifically, versions within a release series that only differ by 
patch number (e.g. 2016.x, 2018.x, etc) are designed to be compatible. I 
would not personally do different processes in the same project with 
different major versions.


-Justin

On 4/10/19 10:56 PM, Bratin Kumar Das wrote:

Thanks

On Wed 10 Apr, 2019, 4:52 PM RAHUL SURESH 
It won't work in lower version than 2016. I don't think it will have any
problem with higher version and influence of the mdrun is not altered I
guess as it is a factor of your mdp settings for higher versions

On Wed 10 Apr, 2019, 3:41 PM Bratin Kumar Das, <
177cy500.bra...@nitk.edu.in>
wrote:


Hi
 Can I run equilibration simulation in one version (ex gromacs2016.5)
and production simulation in other version. Do the version have some
influence in simulation.
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Re: [gmx-users] atom types of hydrogens

[Justin Lemkul]

On 4/10/19 4:12 AM, boshra.moradi.61 wrote:


در 2019-04-09 20:08، Justin Lemkul نوشته است:




On 4/9/19 11:26 AM, boshra.moradi.61 wrote:

  Dear all,

i'm new om gromacs and my molecule is D-glucosamine.i introduced it via
inserting in aminoacids.rtp file.my question is how nominate four
H-atoms . i want atomtypes.atp to find the atometype of these four atoms
but i didn't find.i want you to guide me about this problem,could you



Most force fields should already have parameters for such a species. 
In any case, the information in the .atp file is likely inadequate 
but you can make the assignments based on the same moieties in 
residues defined within the .rtp file.


-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

==


Dear Justin,

Can you clarify this sentence for me, i don't understand what do you 
mean by "  you can make the assignments based on the same moieties in 
residues defined within the .rtp file."


i search .rtp file and i can't find the type of these four hydrogen.in 
addition, the force field is : opls-aa .




You have aliphatic, hydroxyl, and amino hydrogens. Their types can be 
assigned from similar groups. Search the literature to see if there are 
specific parameters for carbohydrates in OPLS-AA. I know there are for 
AMBER and CHARMM.


-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] Protein dipole moments

[Justin Lemkul]

On 4/10/19 1:02 AM, Emran Heshmati wrote:

What are the physical meaning of <|M|^2> and <|M|>^2 in the outputs of gmx
dipoles command ?? Any help is welcome.


The notation suggests the average of the squared dipoles and the square 
of the average dipoles, respectively. Check the source code to be sure.


-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] gromacs instillation

[p buscemi]

when you open a new terminal you need to run " source" again, but you probably 
know this by now
or
add the path to your /etc/.profile to make the change permanent

Sent from Mailspring 
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 the best free email app for work
On Apr 11 2019, at 1:45 am, Mark Abraham  wrote:
> Hi,
>
> Each shell you open needs to be told how to find GROMACS, per
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
>
> Mark
> On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
> > Hello GMX users
> > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> > I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
> > 2019.1.
> > When I open a new terminal and hit gmx, it says gromacs is currently not
> > installed. You can install it by typing: sudo apt install gromacs. When I
> > did it, the version became 5.1.2.
> >
> > Any idea how to solve it!
> > Thank you
> > Ali
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

[Tafelmeier, Stefanie]

Hi Szilárd,

Many thanks, now it is clear to me also how the tests are verified.

This means, I can trust my energy calculation now.

Thanks again,
Steffi


-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Szilárd Páll
Gesendet: Mittwoch, 10. April 2019 23:44
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi,
On Wed, Apr 10, 2019 at 4:19 PM Tafelmeier, Stefanie <
stefanie.tafelme...@zae-bayern.de> wrote:

> Dear Szilárd and Jon,
>
> many thanks for your support.
>
> The system was Ubuntu 18.04 LTS, gcc 7.3 and CUDA 9.2.
> We upgraded now gcc (to 8.2) and CUDA (to 10.1).
>
> Now the regressiontests all pass.
> Also the tests Szilárd ask before are all running. Even just using mdrun
> -nt 80 works.
>

Great, this confirms that there was indeed a strange compatibility issue as
Jon suggested.

Many thanks! It seems that this was the origin of the problem.
>
> Just to be sure, I would like to have a look at the short range value of
> the complex test. As before some passed even without having the right
> values.
>

What do you mean by that?


> Is there a way to compare or a list with the correct outcome?
>

When the regressiontests are executed, the output by default lists all
commands that do the test runs as well as those that verify the outputs,
e.g.

$ perl gmxtest.pl complex
[...]
Testing acetonitrilRF . . . gmx grompp -f ./grompp.mdp -c ./conf -r ./conf
-p ./topol -maxwarn 10  >grompp.out 2>grompp.err
gmx check -s1 ./reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001
>checktpr.out 2>checktpr.err
 gmx mdrun-nb cpu   -notunepme >mdrun.out 2>&1
gmx check -e ./reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05
-lastener Potential >checkpot.out 2>checkpot.err
gmx check -f ./reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05
>checkforce.out 2>checkforce.err
PASSED but check mdp file differences

The gmx check commands do the checking and the the reference_s|d files to
comapre against.

--
Szilárd


> Anyway, here is the link to the tar-ball of the complex folder in case
> there is interest:
> https://it-service.zae-bayern.de/Team/index.php/s/mMyt3MPEfRrn8Ge
>
> Many thanks again for your help.
>
> Best wishes,
> Steffi
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von
> Jonathan Vincent
> Gesendet: Dienstag, 9. April 2019 22:13
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi,
>
> Which operating system are you running on? We have seen some strange
> behavior with large number of threads, gcc 7.3 and a newish version of
> glibc. Specifically the default combination that comes with Ubuntu 18.04
> LTS, but it might be more generic than that.
>
> My suggestion would be to update to gcc 8.3 and CUDA 10.1 (which is
> required for CUDA support of gcc 8), which seemed to fix the problem in
> that case.
>
> If you still have problems we can look at this some more.
>
> Jon
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Szilárd
> Páll
> Sent: 09 April 2019 20:08
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi,
>
> One more test I realized it may be relevant considering that we had a
> similar report earlier this year on similar CPU hardware:
> can you please compile with -DGMX_SIMD=AVX2_256 and rerun the tests?
>
> --
> Szilárd
>
>
> On Tue, Apr 9, 2019 at 8:35 PM Szilárd Páll 
> wrote:
>
> > Dear Stefanie,
> >
> > On Fri, Apr 5, 2019 at 11:48 AM Tafelmeier, Stefanie <
> > stefanie.tafelme...@zae-bayern.de> wrote:
> >
> >> Hi Szilárd,
> >>
> >> thanks for your advices.
> >> I performed the tests.
> >> Both performed without errors.
> >>
> >
> > OK, that excludes simple and obvious issues.
> > Wild guess, but can you run those again, but this time prefix the
> > command with "taskset -c 22-32"
> > ? This makes the tests use cores 22-32 just to check if using a
> > specific set of cores may somehow trigger an error.
> >
> > What CUDA version did you use to compiler the memtest tool -- was it
> > the same (CUDA 9.2) as the one used for building GROMACS?
> >
> > Just to get it right; I have to ask in more detail, because the
> > connection
> >> between is the CPU/GPU and calculation distribution is still a bit
> >> blurry to me:
> >>
> >> If the output of the regressiontests show that the test crashes after
> >> 1-2 steps, this means there is an issue between the transfer between
> >> the CPU and GPU?
> >> As far as I got the short range calculation part is normally split
> >> into nonbonded -> GPU and bonded -> CPU?
> >>
> >
> > The -nb/-pme/-bonded flags control which tasks executes where (if not
> 

Re: [gmx-users] Atom name mismatch between gro and top file

[Dallas Warren]

Simply change the order of the atoms in the gro file to match the topology
file.

The order of the atoms is not in itself what is important, ie they can
really be in any order, it's that the names and order match between
coordinate - topology file and then within the topology file.

This error also typically shows up when the molecule list at the end of the
topology is different to how the molecules are ordered in the coordinate
file.

For example coordinate file has 1x UNK, 1x SOL, 1x UNK then 3,000 SOL. A
topology with a list of the molecules as 2x UNK then 3,001x SOL will throw
up this error.

On Thu, 11 Apr. 2019, 3:00 pm RAHUL SURESH,  wrote:

> Hi Users.
>
> While doing protein-ligand simulation, I get a warning which state
> atom name mismatch between solv.gro and topol.top and name from top file be
> considered and gro will be ignored. Yes, there is a mismatch, as in gro
> file, the atom was in the order C-O-O and in itp file added to top, the
> order was O-C-O. the itp file was generated by prodrg server.
>
> 1. Is it fine to ignore the warning and continue with the simualtion?
>
> 2. If not, which file should i  rename? gro or itp?
>
>
> Thank you
> --
> *Regards,*
> *Rahul *
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Re: [gmx-users] problems with pull code on Martini CG

[Berk Hess]

Hi,

You should not use direction-periodic, you don't want to pull more than half 
the box size, I presume.

Your pull rate is extremely high 50 nm/ns. I would start by lowering this.

Cheers,

Berk


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Bennett 
Addison 
Sent: Thursday, April 11, 2019 12:50 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] problems with pull code on Martini CG

Hello gromacs users,

I am fairly new to MD, trying hard to troubleshoot this issue myself before
posting. But I am at a loss.

I am trying to simulate pulling on a large protein, using Martini CG
simulations and adding the pull code. I am following tutorials for umbrella
sampling (all atom) and for martini protein simulations. Basically, the
exact same setup procedure works when the box size is small, but when I
scale up, things get screwy.

For example: 200 AA protein, placed 50 x 12 x 12 box and pull along X (see
pull code below: using direction-periodic geometry, pull along vector -1.0
0.0 0.0)

gmx editconf -f CG.pdb -o newbox.gro -box 50 12 12 -center 7 6 6

Followed by minimization in vac, solvate, minimize, equilibrate, then
create groups with gmx make_ndx, assign Chain_A as anchored residue, assign
Chain_B as residue to pull, make sure position restraints are correct, and
finally setup and run md_pull.mdp. This simulation works great. I see a
nice unfolding using martini CG model.
Pull code:

; Pull code

pull= yes

pull_ncoords= 1 ; only one reaction coordinate

pull_ngroups= 2 ; two groups defining one reaction
coordinate

pull_group1_name= Chain_A

pull_group2_name= Chain_B

pull_coord1_type= umbrella  ; harmonic potential

pull_coord1_geometry = direction-periodic ;

pull_coord1_vec = -1.0 0.0 0.0

pull_coord1_groups  = 1 2

pull_coord1_start   = yes   ; define initial COM distance > 0

pull_coord1_rate= 0.05  ; 0.05 nm per ps = 5 nm per ns

pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2



Now when I try to replicate the exact same setup but using a larger box (100nm
20nm 20nm) everything fails. When I visualize the trajectory my protein
does not appear to be pulled, but the position output pullx.xvg shows
increase in distance, pullf.xvg shows no changes in force, and if I plot
distance between Chain_A and Chain_B using gmx distance, I see an expected
distance increase.


DOES NOT WORK: gmx editconf -f CG.pdb -o new box.gro -box 100 20 20 -center
8 10 10 (pullx looks ok, but pullf is flat, protein does not extend)

WORKS: gmx editconf -f CG.pdb -o new box.gro -box 50 12 12 -center 5 6 6
(trajectory looks great, pullf and pullx as expected)


Every other parameter / setup procedure is the same, just box size is
different. I need a larger box on my bigger protein (200 AAs) because it
will fully extend past 50nm.


I have tried with two configurations, same issues

- gromacs version 5.1.5 on a computing cluster, single node, AMD with 32
cores

- gromacs version 2018.3 on local machine with intel xeon E5 processors, 40
cores with GPU acceleration


Does anybody know why this may be happening, and how I can get around it?


Thank you!

-Bennett



Dr. Bennett Addison
Manager, SDSU NMR Facility
baddi...@sdsu.edu
206-235-5415  (cell)
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Re: [gmx-users] Energy from a subgroup of molecules

[Mark Abraham]

Hi,

You can't do that with gmx energy, as you need mdrun to understand the new
grouping. But making a new .tpr with the energy groups so defined permits
you to use gmx mdrun -rerun for such a single point energy evaluation.

Mark

On Wed., 10 Apr. 2019, 22:24 p buscemi,  wrote:

>
> Dear Users,
> I've performed an adsorption experiment in which a fraction of molecules
> in solution adsorb to a surface. I can extract the index of those adsorbed,
> and I can obtain the total interaction ( LJ ) of the energy group with the
> surface.
> I can estimate the average interaction of the adsorbed molecules by
> dividing the total energy by the number of molecules within a certain
> distance ( the index number )
> How might I use gmx energy to recalculate the interaction using the
> original surface but only the adsorbed molecules specified in the index
> file... something like
> "gmx energy -f starting.gro -n index.ndx"
>
> A single point calculation would be quite satisfactory.
> thanks
> Paul
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Re: [gmx-users] gromacs instillation

[Mark Abraham]

Hi,

Each shell you open needs to be told how to find GROMACS, per
http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation

Mark

On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:

> Hello GMX users
> I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
> 2019.1.
> When I open a new terminal and hit gmx, it says gromacs is currently not
> installed. You can install it by typing:  sudo apt install gromacs. When I
> did it, the version became 5.1.2.
>
> Any idea how to solve it!
>
> Thank you
> Ali
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Re: [gmx-users] Tpr version check

[Mark Abraham]

Hi,

The old behavior of a graceful rejection of the file with a new version
number is still expected.

The most likely explanation for your observations is that they old version
of gmx is linking somehow to newer versions of things (which also shouldn't
happen ...), and the chimera can't work.
If you can share a tpr on Redmine we can see if there is an issue we can
fix.

Mark

On Wed., 10 Apr. 2019, 23:05 Erik Marklund, 
wrote:

> Hi users,
>
> I accidentally used an older version (2016.3) to run trjconv on some
> trajectories. Some conversions worked, seemingly depending on pbc options
> etc, whereas others stopped with the following output:
>
> Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
>  ->  frame  0 time0.000
> ---
> Program: gmx trjconv, version 2016.3
> Source file: src/gromacs/pbcutil/pbc.cpp (line 94)
>
> Fatal error:
> Unknown ePBC=1051770189 in ePBC2npbcdim
>
> Call me a hopeless nostalgic, but I remember a time when such mistakes
> rendered an error saying that I am using an older version of gmx than the
> version used to generate the tpr file. Is that not a thing anymore, and
> this is the expected behaviour? Seems problematic if gmx tools try to read
> nonsense data (from the viewpoint of the gromacs version used).
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Associate Professor of Biochemistry
> Associate Senior Lecturer in Computational Biochemistry
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4562
> erik.markl...@kemi.uu.se
>
>
>
>
>
>
>
>
>
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