Re: [gmx-users] Can't observe ion separation under the influence of electric field

[David van der Spoel]

Den 2020-02-12 kl. 23:07, skrev Live King:

Dear all,

I am running a simple test case with a lipid bilayer (DMPC), water, and
ions (150mM KCL) under the influence of a constant electric field ( 300mV,
500mV, and 700mV). *I expected positive and negative ions to separate in
the presence of an external electric field*. However, I am not observing
such behavior despite running the all-atom simulation for 400ns in any
case. I am using gromacs 2018.2, my mdp file is standard charmm-gui
production with electric field option.

for example 500mV electric field in Z-direction :
electric-field-z =  0.060  0 0 0 ; *500**mv  = 8.25nm* 0.060 =
500 mV *


Are there any settings to run the electric field simulation that I miss?
Any help will be greatly appreciated.


Did you make density plots to check?

Do you get an output field.xvg that prints the field strength? It may be 
optional though.


The force on the atoms will be quite small still compared to interatomic 
forces therefore the effect may be limited. F = q E (convert to right 
units). In GROMACS MD units a typical interatomic force is ~ 1000 
kJ/mol/nm^2.




Thank you,




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Estimation of configurational entropy

[David van der Spoel]

Den 2020-02-13 kl. 05:10, skrev Pathum Manjula Weerawarna:

Hi everyone,

I'm trying to estimate the configurational entropy of a small molecule using 
gmx anaeig. However, it does not allow me to use a mass-weighted covariance 
matrix for the calculation (only allow me to use mass-unweighted CV matrix). 
Theoretically, the use of a mass unweighted CV matrix for entropy calculation 
is inaccurate (frequencies going to be smaller). Does anybody know the accuracy 
of the entropy calculated using gmx anaeig? Also, is there any way to use a 
mass-weighted CV matrix for this calculation?


The entropy is only the conformational entropy and can therefore be used 
for determining relative entropies, for instance for ligand binding (J 
Chem Theory Comput 9 pp. 4542-4551 (2013)). If you want to compute 
absolute entropies then for now normal mode analysis is the most 
efficient, even though it has limitations as well. See J Phys Chem A. 
122 pp. 8982-8988 (2018).


Sorry to promote my own papers but this is what I know :)



Thank you so much for the help

best
Pathum



Pathum M. Weerawarna, Ph.D.
Postdoctoral Fellow
Silverman Research Group
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston, IL 60208-3113

Phone: (316) 990-8542
Email : pathum.weerawa...@northwestern.edu
  pathumweerawa...@gmail.com
[cid:1e2d5c51-a722-45d1-a750-8b9bf00f3e05]






--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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[gmx-users] Estimation of configurational entropy

[Pathum Manjula Weerawarna]

Hi everyone,

I'm trying to estimate the configurational entropy of a small molecule using 
gmx anaeig. However, it does not allow me to use a mass-weighted covariance 
matrix for the calculation (only allow me to use mass-unweighted CV matrix). 
Theoretically, the use of a mass unweighted CV matrix for entropy calculation 
is inaccurate (frequencies going to be smaller). Does anybody know the accuracy 
of the entropy calculated using gmx anaeig? Also, is there any way to use a 
mass-weighted CV matrix for this calculation?

Thank you so much for the help

best
Pathum



Pathum M. Weerawarna, Ph.D.
Postdoctoral Fellow
Silverman Research Group
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston, IL 60208-3113

Phone: (316) 990-8542
Email : pathum.weerawa...@northwestern.edu
 pathumweerawa...@gmail.com
[cid:1e2d5c51-a722-45d1-a750-8b9bf00f3e05]

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[gmx-users] Can't observe ion separation under the influence of electric field

[Live King]

Dear all,

I am running a simple test case with a lipid bilayer (DMPC), water, and
ions (150mM KCL) under the influence of a constant electric field ( 300mV,
500mV, and 700mV). *I expected positive and negative ions to separate in
the presence of an external electric field*. However, I am not observing
such behavior despite running the all-atom simulation for 400ns in any
case. I am using gromacs 2018.2, my mdp file is standard charmm-gui
production with electric field option.

for example 500mV electric field in Z-direction :
electric-field-z =  0.060  0 0 0 ; *500**mv  = 8.25nm* 0.060 =
500 mV *


Are there any settings to run the electric field simulation that I miss?
Any help will be greatly appreciated.


Thank you,
-- 
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[gmx-users] Tabulated potentials

[Ali Khodayari]

Dear Gromacs users,

I’ve got a question regarding the tabulated potentials for bonded interactions.

Gromacs recognises and reads the non-bonded potential tables through the energy 
groups specified. But how can I refer each bond type to its table?

I have derived coarse-grained potentials for a cellobiose-water system. There 
are 11 beads (4 bead types) in each cellobiose molecule, and each water 
molecule is coarse-grained as one bead. Overall, there are 3 bonded terms for 3 
bond types, 3 anglular potentials for 3 angle types, and 2 dihedral potential 
tables for two types of dihedrals. The tables are named as table_b1.xvg, 
table_b2.xvg, and so on.

Now my question is, how does gromacs recognise which table is regarding which 
bonded term? The simulation crashes at the very beginning giving me the 
following error:

A tabulated bond interaction table number 1 is out of the table range: r
0.511823, between table indices 511 and 512, table length 501

I believe this is caused due to high forces on atoms indeed, but it might be 
also because tables are not specified to the correct bond type.


Kind regards,
Ali
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[gmx-users] Test particle insertion in a specific region

[Sally Li]

Dear Gromacs Users,

I'm now simulating a water droplet with some vacuum space in a NVT
ensemble. I'd like to calculate the excess free energy for different shells
of the droplet via test particle insertion method, which I assume I should
first calculate the COM of the droplet, and then divide the droplet into
different bins and do TPI insertion for different bins.

I'm new ro Gromacs. Could anyone tell me how to do test particle insertion
in specific spherical shells or specific region?

I didn't see region options in TPI integrator. I guess I may miss something.

Thank you in advance.

Best wishes,
Sally
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Re: [gmx-users] generating Doxygen documentation

[Michele Pellegrino]

Paul,

thank you very much!

Cheers,
Michele

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

Sent: 12 February 2020 21:02
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] generating Doxygen documentation

The correct address is
http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml

Need to fix a link somewhere then I think.

/Paul

On Wed, 12 Feb 2020, 20:46 Michele Pellegrino,  wrote:

> Moreover: the link to Jenkins does not work (section 7.8.1, "Building the
> documentation"):
>
>
> http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml
>
> Cheers,
> Michele
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Michele
> Pellegrino 
> Sent: 12 February 2020 20:39
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] generating Doxygen documentation
>
> Mark,
>
> no such directory is produced after make (evein if the output is 'Built
> target doxygen-all').
> The only Doxyfile I can utilize to generate html/latex documentation is
> 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'.
>
> It seems I need to run cmake somewhere, somehow, but it's not really clear
> to me in which directory (and with which options(s)).
>
> Cheers,
> Michele
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 12 February 2020 17:34
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] generating Doxygen documentation
>
> Hi,
>
> When they succeed, the doxygen targets produce files like
>
> $builddir/docs/html/doxygen/html-*/index.xhtml
>
> which you can open in your browser. The doxygen for the released versions
> is on the web however, so it's much easier to just use or refer to that.
>
> Mark
>
> On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:
>
> > Hi,
> >
> >
> > I am trying to generate the Doxygen documentation for GROMACS from the
> > files in /docs/doxygen.
> >
> > I following 2020 manual, I run 'make doxygen-all' in the build directory,
> > succesfully; I don't know what to do next: I tried to run cmake in the
> > doxygen directory to generate the Doxyfiles, but I get the following
> errors:
> >
> > """
> >
> > CMake Error at CMakeLists.txt:36 (include):
> >   include could not find load file:
> >
> > gmxCustomCommandUtilities
> >
> >
> > CMake Error at CMakeLists.txt:37 (include):
> >   include could not find load file:
> >
> > gmxOptionUtilities
> >
> >
> > CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
> >   Unknown CMake command "gmx_dependent_option".
> >
> > """
> >
> > What should I do?
> >
> >
> > Thanks for your attention,
> >
> > Michele
> >
> >
> > p.s. I am referring to the github master branch current version
> > --
> > 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
> --
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> posting!
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Re: [gmx-users] generating Doxygen documentation

[Paul Bauer]

The correct address is
http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml

Need to fix a link somewhere then I think.

/Paul

On Wed, 12 Feb 2020, 20:46 Michele Pellegrino,  wrote:

> Moreover: the link to Jenkins does not work (section 7.8.1, "Building the
> documentation"):
>
>
> http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml
>
> Cheers,
> Michele
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Michele
> Pellegrino 
> Sent: 12 February 2020 20:39
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] generating Doxygen documentation
>
> Mark,
>
> no such directory is produced after make (evein if the output is 'Built
> target doxygen-all').
> The only Doxyfile I can utilize to generate html/latex documentation is
> 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'.
>
> It seems I need to run cmake somewhere, somehow, but it's not really clear
> to me in which directory (and with which options(s)).
>
> Cheers,
> Michele
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 12 February 2020 17:34
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] generating Doxygen documentation
>
> Hi,
>
> When they succeed, the doxygen targets produce files like
>
> $builddir/docs/html/doxygen/html-*/index.xhtml
>
> which you can open in your browser. The doxygen for the released versions
> is on the web however, so it's much easier to just use or refer to that.
>
> Mark
>
> On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:
>
> > Hi,
> >
> >
> > I am trying to generate the Doxygen documentation for GROMACS from the
> > files in /docs/doxygen.
> >
> > I following 2020 manual, I run 'make doxygen-all' in the build directory,
> > succesfully; I don't know what to do next: I tried to run cmake in the
> > doxygen directory to generate the Doxyfiles, but I get the following
> errors:
> >
> > """
> >
> > CMake Error at CMakeLists.txt:36 (include):
> >   include could not find load file:
> >
> > gmxCustomCommandUtilities
> >
> >
> > CMake Error at CMakeLists.txt:37 (include):
> >   include could not find load file:
> >
> > gmxOptionUtilities
> >
> >
> > CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
> >   Unknown CMake command "gmx_dependent_option".
> >
> > """
> >
> > What should I do?
> >
> >
> > Thanks for your attention,
> >
> > Michele
> >
> >
> > p.s. I am referring to the github master branch current version
> > --
> > 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> --
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>
> * Please search the archive at
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> posting!
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>
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Re: [gmx-users] generating Doxygen documentation

[Michele Pellegrino]

Moreover: the link to Jenkins does not work (section 7.8.1, "Building the 
documentation"):

http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml

Cheers,
Michele

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Michele 
Pellegrino 
Sent: 12 February 2020 20:39
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] generating Doxygen documentation

Mark,

no such directory is produced after make (evein if the output is 'Built target 
doxygen-all').
The only Doxyfile I can utilize to generate html/latex documentation is 
'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'.

It seems I need to run cmake somewhere, somehow, but it's not really clear to 
me in which directory (and with which options(s)).

Cheers,
Michele

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

Sent: 12 February 2020 17:34
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] generating Doxygen documentation

Hi,

When they succeed, the doxygen targets produce files like

$builddir/docs/html/doxygen/html-*/index.xhtml

which you can open in your browser. The doxygen for the released versions
is on the web however, so it's much easier to just use or refer to that.

Mark

On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:

> Hi,
>
>
> I am trying to generate the Doxygen documentation for GROMACS from the
> files in /docs/doxygen.
>
> I following 2020 manual, I run 'make doxygen-all' in the build directory,
> succesfully; I don't know what to do next: I tried to run cmake in the
> doxygen directory to generate the Doxyfiles, but I get the following errors:
>
> """
>
> CMake Error at CMakeLists.txt:36 (include):
>   include could not find load file:
>
> gmxCustomCommandUtilities
>
>
> CMake Error at CMakeLists.txt:37 (include):
>   include could not find load file:
>
> gmxOptionUtilities
>
>
> CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
>   Unknown CMake command "gmx_dependent_option".
>
> """
>
> What should I do?
>
>
> Thanks for your attention,
>
> Michele
>
>
> p.s. I am referring to the github master branch current version
> --
> 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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] generating Doxygen documentation

[Michele Pellegrino]

Mark,

no such directory is produced after make (evein if the output is 'Built target 
doxygen-all').
The only Doxyfile I can utilize to generate html/latex documentation is 
'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'.

It seems I need to run cmake somewhere, somehow, but it's not really clear to 
me in which directory (and with which options(s)).

Cheers,
Michele

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

Sent: 12 February 2020 17:34
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] generating Doxygen documentation

Hi,

When they succeed, the doxygen targets produce files like

$builddir/docs/html/doxygen/html-*/index.xhtml

which you can open in your browser. The doxygen for the released versions
is on the web however, so it's much easier to just use or refer to that.

Mark

On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:

> Hi,
>
>
> I am trying to generate the Doxygen documentation for GROMACS from the
> files in /docs/doxygen.
>
> I following 2020 manual, I run 'make doxygen-all' in the build directory,
> succesfully; I don't know what to do next: I tried to run cmake in the
> doxygen directory to generate the Doxyfiles, but I get the following errors:
>
> """
>
> CMake Error at CMakeLists.txt:36 (include):
>   include could not find load file:
>
> gmxCustomCommandUtilities
>
>
> CMake Error at CMakeLists.txt:37 (include):
>   include could not find load file:
>
> gmxOptionUtilities
>
>
> CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
>   Unknown CMake command "gmx_dependent_option".
>
> """
>
> What should I do?
>
>
> Thanks for your attention,
>
> Michele
>
>
> p.s. I am referring to the github master branch current version
> --
> 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] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)

[Jihong Ma]

Sounds good. Thanks.

On Wed, Feb 12, 2020 at 1:22 PM Paul bauer  wrote:

> Hello,
>
> please do ***NOT*** use the mailing list for those kinds of
> announcements in the future.
> It is supposed to be for people discussing and asking for help with
> GROMACS, not for advertising conferences.
>
> Thanks
>
> Paul
>
> On 12/02/2020 19:13, Jihong Ma wrote:
> > Dear colleagues,
> >
> > The Society of Engineering Science (SES) 57th Annual Technical Meeting
> will
> > be held at Hyatt Regency Minneapolis, September 28-30, 2020 (
> > https://ccaps.umn.edu/SES).
> >
> > As part of this meeting, we are organizing a mini-symposium addressing
> > the *advances
> > in polymer modeling and simulations* under Track 7 - Soft, Active
> Materials
> > and Applications in Soft Robotics.
> >
> > The production of newer classes of polymers, such as polymerized ionic
> > liquids and nanoporous polymers, opened up exciting possibilities for
> > various applications including electrochemical energy generation and
> > storage, water purification, sensing and releasing biological molecules,
> > development of light-weight structures. Modeling these complex
> > architectures presents significant challenges related, for instance, to
> the
> > system size, accuracy of the classical and coarse-grained potentials,
> > presence of multi-scale effects, and critical discrepancies with
> experiment.
> >
> > This mini-symposium aims to bring together scientists and engineers
> working
> > at the forefront of the modeling and simulation to exchange and share
> their
> > experiences and recent research results.
> >
> > We cordially invite all the interested scholars to submit your abstract
> to
> > this mini-symposium. The deadline for submission is *March 17, 2020*.
> >
> > We look forward to your presentations at our symposium.
> >
> >
> >
> > Best regards,
> >
> > Jihong Ma, University of Vermont
> >
> > Traian Dumitrica, University of Minnesota - Twin Cities
>
>
> --
> Paul Bauer, PhD
> GROMACS Development Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] generating Doxygen documentation

[Sergio Perez]

I'm using

Ubuntu 18.04.3 LTS

On Wed, Feb 12, 2020 at 7:52 PM Benson Muite 
wrote:

>
> Hi,
> What platform are you building on? Last time I tried this, there were a
> few extra dependencies I needed to install.
> Benson
>
> On Thu, Feb 13, 2020, at 12:34 AM, Mark Abraham wrote:
> > Hi,
> >
> > When they succeed, the doxygen targets produce files like
> >
> > $builddir/docs/html/doxygen/html-*/index.xhtml
> >
> > which you can open in your browser. The doxygen for the released versions
> > is on the web however, so it's much easier to just use or refer to that.
> >
> > Mark
> >
> > On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:
> >
> > > Hi,
> > >
> > >
> > > I am trying to generate the Doxygen documentation for GROMACS from the
> > > files in /docs/doxygen.
> > >
> > > I following 2020 manual, I run 'make doxygen-all' in the build
> directory,
> > > succesfully; I don't know what to do next: I tried to run cmake in the
> > > doxygen directory to generate the Doxyfiles, but I get the following
> errors:
> > >
> > > """
> > >
> > > CMake Error at CMakeLists.txt:36 (include):
> > >   include could not find load file:
> > >
> > > gmxCustomCommandUtilities
> > >
> > >
> > > CMake Error at CMakeLists.txt:37 (include):
> > >   include could not find load file:
> > >
> > > gmxOptionUtilities
> > >
> > >
> > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
> > >   Unknown CMake command "gmx_dependent_option".
> > >
> > > """
> > >
> > > What should I do?
> > >
> > >
> > > Thanks for your attention,
> > >
> > > Michele
> > >
> > >
> > > p.s. I am referring to the github master branch current version
> > > --
> > > 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.
> >
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> posting!
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Re: [gmx-users] generating Doxygen documentation

[Benson Muite]

Hi,
What platform are you building on? Last time I tried this, there were a few 
extra dependencies I needed to install.
Benson

On Thu, Feb 13, 2020, at 12:34 AM, Mark Abraham wrote:
> Hi,
> 
> When they succeed, the doxygen targets produce files like
> 
> $builddir/docs/html/doxygen/html-*/index.xhtml
> 
> which you can open in your browser. The doxygen for the released versions
> is on the web however, so it's much easier to just use or refer to that.
> 
> Mark
> 
> On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:
> 
> > Hi,
> >
> >
> > I am trying to generate the Doxygen documentation for GROMACS from the
> > files in /docs/doxygen.
> >
> > I following 2020 manual, I run 'make doxygen-all' in the build directory,
> > succesfully; I don't know what to do next: I tried to run cmake in the
> > doxygen directory to generate the Doxyfiles, but I get the following errors:
> >
> > """
> >
> > CMake Error at CMakeLists.txt:36 (include):
> >   include could not find load file:
> >
> > gmxCustomCommandUtilities
> >
> >
> > CMake Error at CMakeLists.txt:37 (include):
> >   include could not find load file:
> >
> > gmxOptionUtilities
> >
> >
> > CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
> >   Unknown CMake command "gmx_dependent_option".
> >
> > """
> >
> > What should I do?
> >
> >
> > Thanks for your attention,
> >
> > Michele
> >
> >
> > p.s. I am referring to the github master branch current version
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
> 
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> 
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] lmfit not working

[Sergio Perez]

Dear gmx comunity,

I am trying to use gmx analyze for the block analysis and I get this error:
Fatal error:
This build of GROMACS was not configured with support for lmfit, so the
requested fitting cannot be performed. See the install guide for
instructions
on how to build GROMACS with lmfit supported.

I have installed gromacs with the option -DGMX_USE_LMFIT=INTERNAL, so I am
guessing I don't need to install anything in addition. I have tryed both
2019.4 and 2020 but the same happens. I saw on redmine there had been
issues with this. Should I post this on redmine?
Thanks a lot!
Sergio
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Re: [gmx-users] runtime error: pdb2gmx issues in Python API

[Eric Irrgang]

Hi Marko,

I apologize for the slow response.

"pdb2gmx" is not an executable, but an argument. Try

gmx.commandline_operation(
'gmx',
['pdb2gmx', '-water', 'spce', '-ff', 'oplsaa']
...)

I hope to be able to improve the documentation soon, but the exception
should have been more helpful. I have created issue #3376 at
https://redmine.gromacs.org/issues/3376

Best,
Eric

On Tue, Feb 4, 2020 at 5:55 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

>
> test=gmx.commandline_operation(executable = "pdb2gmx",
>   arguments = ["-water", "spce"
>,"-ff", "oplsaa"
>]
> ...
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Re: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)

[Paul bauer]

Hello,

please do ***NOT*** use the mailing list for those kinds of 
announcements in the future.
It is supposed to be for people discussing and asking for help with 
GROMACS, not for advertising conferences.


Thanks

Paul

On 12/02/2020 19:13, Jihong Ma wrote:

Dear colleagues,

The Society of Engineering Science (SES) 57th Annual Technical Meeting will
be held at Hyatt Regency Minneapolis, September 28-30, 2020 (
https://ccaps.umn.edu/SES).

As part of this meeting, we are organizing a mini-symposium addressing
the *advances
in polymer modeling and simulations* under Track 7 - Soft, Active Materials
and Applications in Soft Robotics.

The production of newer classes of polymers, such as polymerized ionic
liquids and nanoporous polymers, opened up exciting possibilities for
various applications including electrochemical energy generation and
storage, water purification, sensing and releasing biological molecules,
development of light-weight structures. Modeling these complex
architectures presents significant challenges related, for instance, to the
system size, accuracy of the classical and coarse-grained potentials,
presence of multi-scale effects, and critical discrepancies with experiment.

This mini-symposium aims to bring together scientists and engineers working
at the forefront of the modeling and simulation to exchange and share their
experiences and recent research results.

We cordially invite all the interested scholars to submit your abstract to
this mini-symposium. The deadline for submission is *March 17, 2020*.

We look forward to your presentations at our symposium.



Best regards,

Jihong Ma, University of Vermont

Traian Dumitrica, University of Minnesota - Twin Cities



--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)

[Jihong Ma]

Dear colleagues,

The Society of Engineering Science (SES) 57th Annual Technical Meeting will
be held at Hyatt Regency Minneapolis, September 28-30, 2020 (
https://ccaps.umn.edu/SES).

As part of this meeting, we are organizing a mini-symposium addressing
the *advances
in polymer modeling and simulations* under Track 7 - Soft, Active Materials
and Applications in Soft Robotics.

The production of newer classes of polymers, such as polymerized ionic
liquids and nanoporous polymers, opened up exciting possibilities for
various applications including electrochemical energy generation and
storage, water purification, sensing and releasing biological molecules,
development of light-weight structures. Modeling these complex
architectures presents significant challenges related, for instance, to the
system size, accuracy of the classical and coarse-grained potentials,
presence of multi-scale effects, and critical discrepancies with experiment.

This mini-symposium aims to bring together scientists and engineers working
at the forefront of the modeling and simulation to exchange and share their
experiences and recent research results.

We cordially invite all the interested scholars to submit your abstract to
this mini-symposium. The deadline for submission is *March 17, 2020*.

We look forward to your presentations at our symposium.



Best regards,

Jihong Ma, University of Vermont

Traian Dumitrica, University of Minnesota - Twin Cities
-- 
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Re: [gmx-users] generating Doxygen documentation

[Mark Abraham]

Hi,

When they succeed, the doxygen targets produce files like

$builddir/docs/html/doxygen/html-*/index.xhtml

which you can open in your browser. The doxygen for the released versions
is on the web however, so it's much easier to just use or refer to that.

Mark

On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:

> Hi,
>
>
> I am trying to generate the Doxygen documentation for GROMACS from the
> files in /docs/doxygen.
>
> I following 2020 manual, I run 'make doxygen-all' in the build directory,
> succesfully; I don't know what to do next: I tried to run cmake in the
> doxygen directory to generate the Doxyfiles, but I get the following errors:
>
> """
>
> CMake Error at CMakeLists.txt:36 (include):
>   include could not find load file:
>
> gmxCustomCommandUtilities
>
>
> CMake Error at CMakeLists.txt:37 (include):
>   include could not find load file:
>
> gmxOptionUtilities
>
>
> CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
>   Unknown CMake command "gmx_dependent_option".
>
> """
>
> What should I do?
>
>
> Thanks for your attention,
>
> Michele
>
>
> p.s. I am referring to the github master branch current version
> --
> 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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[gmx-users] generating Doxygen documentation

[Michele Pellegrino]

Hi,


I am trying to generate the Doxygen documentation for GROMACS from the files in 
/docs/doxygen.

I following 2020 manual, I run 'make doxygen-all' in the build directory, 
succesfully; I don't know what to do next: I tried to run cmake in the doxygen 
directory to generate the Doxyfiles, but I get the following errors:

"""

CMake Error at CMakeLists.txt:36 (include):
  include could not find load file:

gmxCustomCommandUtilities


CMake Error at CMakeLists.txt:37 (include):
  include could not find load file:

gmxOptionUtilities


CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
  Unknown CMake command "gmx_dependent_option".

"""

What should I do?


Thanks for your attention,

Michele


p.s. I am referring to the github master branch current version
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Re: [gmx-users] Protein stabilization

[Justin Lemkul]

On 2/12/20 6:20 AM, Gonzalez Fernandez, Cristina wrote:

Dear Gromacs users,


I'm trying to perform a protein-lipid complex simulation. While the interaction 
between these molecules seems reasonable, the protein Root Mean Square 
Deviation is too high, and I don't know how to stabilice it. Could you 
recommend me any simulation trick to stabilize the protein and improve the 
simulation?



If only such a magic wand existed that made our unexpected outcomes turn 
into something we want :)


If a simulation does not reproduce known behavior, something is wrong 
with the model, its preparation, the force field parameters, simulation 
is too short, etc.


-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] Experimental to Simulation Time Period Conversion

[Justin Lemkul]

On 2/12/20 8:23 AM, Peter Mawanga wrote:

Thanks a lot sir for your reply.

Since experiments take place over hours but the simulations can at best
approach millisecond levels. I was wondering if there is an acceptable time
conversion factor from experiments to simulations. For example, the
simulation data generated over a 350 ns period can be taken as an
acceptable representation of a 24 hours long experiment.


No, I think there is no justification for such a statement. The time 
scales are entirely different.


Simulations can only address questions within the accessible time 
regime. Enhanced sampling methods may help you better sample states that 
would only be otherwise observed via impractically long simulations, but 
you often lose the kinetic argument in favor of thermodynamics (i.e. you 
can describe the ensemble but not the time taken to interconvert between 
different states).


-Justin


On Wed, Feb 12, 2020 at 12:52 PM John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:


Dear group members

My sincere apologies for the non-Gromacs related question, but I require
this information urgently and hence posted my query here.

Could someone please provide me with any guidelines to appropriately

model

experimental processes with molecular dynamics simulations?

What experimental processes are you talking about? Most timescales of
interest for physical processes range from picoseconds to seconds to
thousands of years. As you note, most timescales are out of reach of MD
(simulating anything interesting over the microsecond timescale is
extremely difficult).


Since the simulation periods are usually much shorter than the
experimental
time scales, I was searching for a generally acceptable time reduction
factor or some literature towards that direction.

What do you mean by "time reduction factor"? What exactly are you doing?
There are enhanced sampling methods which sort of "accelerate" the pace of
the process/system you are studying... Perhaps looking in that direction
might give you some ideas.

Best,

John


Any information or suggestion would be greatly appreciated.

--
Cheers
Peter
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send

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



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





--
==

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] Query

[Justin Lemkul]

On 2/11/20 4:46 PM, sai manohar wrote:

You cannot generate the desired parameters (.itp) for metals in the ATB
server. In fact even CGenFF or RED server are also not useful for metals.
However, if you have access to any DFT modeling in house to perform QM
calculations using Gaussian etc., you can generate/build your own force
field for these particular kind of molecules.

Hope that's helpful.


To add on to this, one would not parametrize ferric citrate, but would 
instead parametrize citrate (which CGenFF and other servers can handle) 
and Fe3+ separately (based on free energy of hydration or whatever other 
experimental data exist) and then verify that the interactions between 
the ion and relevant ligand and protein moieties is adequately described 
(against QM, usually).


-Justin


On Tue, Feb 11, 2020, 18:23 Neha Tiwari  wrote:


Dear Gromacs Experts,
I want to parametrize Ferric citrate and have already performed DFT
calculations using different basis sets, but I am unable to upload the
refined molecule on, ATB so that I can get its topology files to proceed
further.
Please help.

Thanks in advance.
Neha.
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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] Experimental to Simulation Time Period Conversion

[Peter Mawanga]

Thanks a lot sir for your reply.

Since experiments take place over hours but the simulations can at best
approach millisecond levels. I was wondering if there is an acceptable time
conversion factor from experiments to simulations. For example, the
simulation data generated over a 350 ns period can be taken as an
acceptable representation of a 24 hours long experiment.

On Wed, Feb 12, 2020 at 12:52 PM John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:

> > Dear group members
> >
> > My sincere apologies for the non-Gromacs related question, but I require
> > this information urgently and hence posted my query here.
> >
> > Could someone please provide me with any guidelines to appropriately
> model
> > experimental processes with molecular dynamics simulations?
>
> What experimental processes are you talking about? Most timescales of
> interest for physical processes range from picoseconds to seconds to
> thousands of years. As you note, most timescales are out of reach of MD
> (simulating anything interesting over the microsecond timescale is
> extremely difficult).
>
> >
> > Since the simulation periods are usually much shorter than the
> > experimental
> > time scales, I was searching for a generally acceptable time reduction
> > factor or some literature towards that direction.
>
> What do you mean by "time reduction factor"? What exactly are you doing?
> There are enhanced sampling methods which sort of "accelerate" the pace of
> the process/system you are studying... Perhaps looking in that direction
> might give you some ideas.
>
> Best,
>
> John
>
> >
> > Any information or suggestion would be greatly appreciated.
> >
> > --
> > Cheers
> > Peter
> > --
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> >
>
>
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-- 
Cheers
Peter
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Re: [gmx-users] Experimental to Simulation Time Period Conversion

[John Whittaker]

> Dear group members
>
> My sincere apologies for the non-Gromacs related question, but I require
> this information urgently and hence posted my query here.
>
> Could someone please provide me with any guidelines to appropriately model
> experimental processes with molecular dynamics simulations?

What experimental processes are you talking about? Most timescales of
interest for physical processes range from picoseconds to seconds to
thousands of years. As you note, most timescales are out of reach of MD
(simulating anything interesting over the microsecond timescale is
extremely difficult).

>
> Since the simulation periods are usually much shorter than the
> experimental
> time scales, I was searching for a generally acceptable time reduction
> factor or some literature towards that direction.

What do you mean by "time reduction factor"? What exactly are you doing?
There are enhanced sampling methods which sort of "accelerate" the pace of
the process/system you are studying... Perhaps looking in that direction
might give you some ideas.

Best,

John

>
> Any information or suggestion would be greatly appreciated.
>
> --
> Cheers
> Peter
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> Gromacs Users mailing list
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> posting!
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>


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[gmx-users] Protein stabilization

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,


I'm trying to perform a protein-lipid complex simulation. While the interaction 
between these molecules seems reasonable, the protein Root Mean Square 
Deviation is too high, and I don't know how to stabilice it. Could you 
recommend me any simulation trick to stabilize the protein and improve the 
simulation?


Thank you in advance!!


Cristina
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[gmx-users] Experimental to Simulation Time Period Conversion

[Peter Mawanga]

Dear group members

My sincere apologies for the non-Gromacs related question, but I require
this information urgently and hence posted my query here.

Could someone please provide me with any guidelines to appropriately model
experimental processes with molecular dynamics simulations?

Since the simulation periods are usually much shorter than the experimental
time scales, I was searching for a generally acceptable time reduction
factor or some literature towards that direction.

Any information or suggestion would be greatly appreciated.

-- 
Cheers
Peter
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Re: [gmx-users] Free energy perturbation of ligand

[Alessandra Villa]

Hi,

On Wed, Feb 12, 2020 at 8:54 AM TIASHA ADHIKARY  wrote:

> Hello,
> I am trying to calculate FEP using gromacs. I have used pmx for initial
> structure and .itp file.
> I am getting the following warning
>
> WARNING 1 [file MOL.itp, line 185]:
>   Some parameters for bonded interaction involving perturbed atoms are
>   specified explicitly in state A, but not B - copying A to B
>
> Even if I ignore this warning, structure is not minimizing.
>
> "Steepest Descents converged to machine precision in 185 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  =  1.8540598e+08
> Maximum force =  5.4468039e+04 on atom 6
> Norm of force =  2.0960916e+03"
>
> My guess is that your problem is in energy minimization step and not in
free energy calculation (NOTE I am not familiar with pmx). The warning does
not affect your energy minimization.
If you  perform the energy minimization without state B, you should get the
same.
To solve the problem, you could modify energy minimization setting (maybe
you could use other methods or changing  the criteria - see below) or/and
check that there is not something "wrong" in your starting structure.

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=steep#run-control

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=steep#energy-minimization

Best regards
Alessandra



> I am not understanding how to solve this error. I will be highly obliged
> if anybody help me.
>
> Thanks in advance.
>
> Regards,
> Tiasha Adhikary
> M.Tech, IIT Guwahati
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