Re: [gmx-users] GROMACS 2020.1 failed to pass make check

[Wei-Tse Hsu]

Hi Paul,
Thank you so much for your reply! That is very helpful.

Best,
Wei-Tse

On Mon, Apr 6, 2020 at 1:23 AM Paul bauer  wrote:

> Hello,
>
> you are using a plumed modified version that adds extra options to mdrun.
> Our unit tests check that the output from mdrun -h stays invariant, and
> this is no longer the case once you modify the code for plumed.
>
> You can ignore this failure in this case, but please mention in the
> future if you are using modified versions of the code.
>
> Cheers
>
> Paul
>
> On 05/04/2020 21:23, Wei-Tse Hsu wrote:
> > Dear gmx users,
> > Recently I've been trying to install GROMACS 20201. After successfully
> > compilng GROMACS 2020.1, when executing make check command, I
> > encountered the following error. Specifically, one out of 56 tests
> failed,
> > which was related to Mdrun Test.WritesHelp. Looking at the error message,
> > I'm still not sure what it means and how I should solve this problem. I
> > wonder if anyone had this before that could give me some insights about
> how
> > I could solve the problem. Any help would be appreciated!
> >
> > Here is the error message in the middle.
> >
> >
> >
> >
> >
> > *[--] 1 test from MdrunTest[ RUN  ]
> >
> MdrunTest.WritesHelp/home/wei-tse/Documents/Software/GROMACS/gromacs-2020.1/src/testutils/refdata.cpp:867:
> > Failure  In item: /Help string   Actual: 'SYNOPSIS*
> > And here is the error message in the end.
> >
> >
> >
> >
> >
> > *The following tests FAILED: 43 - MdrunTests
> > (Failed)CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> > 'CMakeFiles/run-ctest-nophys' failedCMakeFiles/Makefile2:1467: recipe for
> > target 'CMakeFiles/run-ctest-nophys.dir/all'
> > failedCMakeFiles/Makefile2:445: recipe for target
> > 'CMakeFiles/check.dir/rule' failedMakefile:327: recipe for target 'check'
> > failed*
> >
> > And here is the whole STDOUT message of the command printed by make
> *check
> >> make_check.log*.
> >
> https://drive.google.com/file/d/1Nb2BLzA2Vl_cjS1b_M_HNk0wkrfR2WKt/view?usp=sharing
> >
> > Best,
> > Wei-Tse
>
>
> --
> Paul Bauer, PhD
> GROMACS Development Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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Re: [gmx-users] How to parametrize a new molecule?

[Herbert de Castro Georg]

Thanks, Mahdi.

I'm aware of that study. Actually it's because of it that I have chosen the
latest CHARMM27 for the simulations.

Best,
Herbert

Em sáb., 4 de abr. de 2020 às 12:57, Mahdi Bagherpoor 
escreveu:

> Hello Herbert,
>
> Not related to your question, but be careful if you are going to use
> CHARMM36 force field for DNA, as a recent study (
> https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does
> not preserve DNA stability at a longer time scale, in case you are going to
> do so.
>
> Best,
> Mahdi
>
> On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg 
> wrote:
>
> > Thanks, Justin!
> >
> >
> >
> > Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul 
> > escreveu:
> >
> > >
> > >
> > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote:
> > > > Dear users,
> > > >
> > > > I want to perform a simulation of a molecule inside DNA. I'm probably
> > > going
> > > > to use CHARMM for DNA. But how do I parametrize the molecule?
> > >
> > > http://cgenff.umaryland.edu/
> > >
> > > -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] Velocities from the .gro file

[Justin Lemkul]

On 4/6/20 12:16 PM, Mohamed Abdelaal wrote:

Hello everybody :)

Can I use the gmx insert-molecules to insert molecules in my box with
velocities by adding the velocities in the .gro file and insert the
molecules from this .gro file ?


Have you tried it?

-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.
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[gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

Hello everybody :)

Can I use the gmx insert-molecules to insert molecules in my box with
velocities by adding the velocities in the .gro file and insert the
molecules from this .gro file ?

Thanks

Mohamed
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[gmx-users] restarting a simulation

[Sadaf Rani]

Dear Gromacs users
I am restarting a simulation with the following command:-
mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append

However, I am getting following error message. All the below-named files
are there in my directory but it still complains the same.

Inconsistency in user input:
Some output files listed in the checkpoint file md10_prev.cpt are not
present
or not named as the output files by the current program:)Expected output
files
that are present:

Expected output files that are not present or named differently:
md10.log
md10.xtc
md10.trr
md10.edr
md10.xvg
To keep your simulation files safe, this simulation will not restart. Either
name your
output files exactly the same as the previous simulation part (e.g. with
-deffnm), or
make sure all the output files are present (e.g. run from the same directory
as the
previous simulation part), or instruct mdrun to write new output files with
mdrun -noappend.
In the last case, you will not be able to use appending in future for this
simulation.

 I also tried without -append option.
Please correct me if I am wrong somewhere.
Thanks.

Sadaf
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Re: [gmx-users] Fumbling in the dark with dihedral pulling

[Justin Lemkul]

On 4/6/20 10:53 AM, Marko Petrovic wrote:

Thank you.

I updated the mdp file. (Is the dihedral  defined as a pair of planes rather 
than a triplet of vectors?)


Perhaps my interpretation of the documentation was incorrect; I thought 
the planes were supposed to be defined, but I suppose it's defined by 
vectors instead.


http://manual.gromacs.org/current/user-guide/mdp-options.html#com-pulling



Unfortunately I still get the segmentation fault and similar warnings. I will 
try to compile the differences between the sample mdp and the one I used, then 
see which differences I can not understand and then just ask about those.


Does your simulation run without pulling options? A sanity check is 
wise. Then test with only one dihedral restrained. It's possible 
something is buggy; I don't know how widely used the dihedral pulling is 
used, and I have not used it personally.


-Justin


With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

On 6 Apr 2020, at 14:44, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 4/6/20 2:33 AM, Marko Petrovic wrote:
I figure it might be helpful to see my other files so I include a link:
https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin


Your dihedral definitions are simply incorrect.

pull_coord1_groups = 1 2 2 3 3 4
pull_coord2_groups = 2 3 3 4 4 5 should be
pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -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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--
==

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] Fumbling in the dark with dihedral pulling

[Marko Petrovic]

Thank you.

I updated the mdp file. (Is the dihedral  defined as a pair of planes rather 
than a triplet of vectors?) Unfortunately I still get the segmentation fault 
and similar warnings. I will try to compile the differences between the sample 
mdp and the one I used, then see which differences I can not understand and 
then just ask about those.

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

On 6 Apr 2020, at 14:44, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 4/6/20 2:33 AM, Marko Petrovic wrote:
I figure it might be helpful to see my other files so I include a link:
https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin


Your dihedral definitions are simply incorrect.

pull_coord1_groups = 1 2 2 3 3 4
pull_coord2_groups = 2 3 3 4 4 5 should be
pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -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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[gmx-users] Anharmonic/Morse flexible water

[Jacek Artur Kozuch]

Hi all,

I am currently trying out various water models for some solute/solvent
systems and I was wondering if there are any (reliable) anharmonic/Morse
flexbile water models that can be used in Gromacs?

I've seen that can set [ Morse ] for bonds, but don't want to start doing
random changes to available models.

Thanks in advance and stay healthy!

Best,
Jacek

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Re: [gmx-users] Bonds definition in itp files

[Justin Lemkul]

On 4/6/20 9:55 AM, Sina Omrani wrote:

Thanks, dear Justin. if I define a constraint on a bond then force constant
isn't useless?


Yes, because you no longer have a harmonic interaction. It is a fixed 
length. Whether or not the bond should be constrained is dictated by 
whether or not the force field applies constraints to all bonds or only 
bonds to H. If the latter, you shouldn't apply ad hoc constraints.


-Justin


On Mon, 6 Apr 2020 at 17:12, Justin Lemkul  wrote:



On 4/6/20 7:24 AM, Sina Omrani wrote:

Hi,
I wanted to know how we specify a bond order in our simulation? For
example, if we have a triple bond in our structure between atoms 1 and 2,
is it by length and force constants or we define 1 and 2 bonds three

times

in the bond section of itp file?
What if we use a constraint on this bond? because I get better results

when

I define the bond three times but haven't seen this method. is it wrong?

All interactions should be defined only once, and the parameters used
should produce correct behavior. MM force fields have no concept of
double or triple bonds; they only know the stiffness of the spring
connecting the atoms. My guess is that if you had to add the bond three
times, the force field parameters are adding together, indicating that
the force constant is unsuitable for what you're trying to and needs to
be refined.

-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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--
==

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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] Bonds definition in itp files

[Sina Omrani]

Thanks, dear Justin. if I define a constraint on a bond then force constant
isn't useless?

On Mon, 6 Apr 2020 at 17:12, Justin Lemkul  wrote:

>
>
> On 4/6/20 7:24 AM, Sina Omrani wrote:
> > Hi,
> > I wanted to know how we specify a bond order in our simulation? For
> > example, if we have a triple bond in our structure between atoms 1 and 2,
> > is it by length and force constants or we define 1 and 2 bonds three
> times
> > in the bond section of itp file?
> > What if we use a constraint on this bond? because I get better results
> when
> > I define the bond three times but haven't seen this method. is it wrong?
>
> All interactions should be defined only once, and the parameters used
> should produce correct behavior. MM force fields have no concept of
> double or triple bonds; they only know the stiffness of the spring
> connecting the atoms. My guess is that if you had to add the bond three
> times, the force field parameters are adding together, indicating that
> the force constant is unsuitable for what you're trying to and needs to
> be refined.
>
> -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] Multi-GPU optimization, "DD without halo exchange is not supported"

[Szilárd Páll]

On Fri, Mar 27, 2020 at 8:30 PM Leandro Bortot 
wrote:

> Dear users,
>
>  I'm trying to optimize the execution of a system composed by 10
> million atoms on a multi-GPU machine with GROMACS 2020.1.
>  I've followed the instructions given at
>
> https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/
> . However, when I run my simulation, mdrun tells me this:
>
> "
>
> *Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU
> environment variable, but the following condition(s) were not
> satisfied:Domain decomposition without GPU halo exchange is not supported.*
> "
>
>  My understanding was that exporting *GMX_GPU_DD_COMMS=true* would
> enable such halo communications.
>  My simulation runs, however the performance is not scaling well with
> the number of GPUs.
>
>  I've done the following:
> "
>
> *export GMX_GPU_DD_COMMS=trueexport GMX_GPU_PME_PP_COMMS=trueexport
> GMX_FORCE_UPDATE_DEFAULT_GPU=true*"
>

You are getting the error below because you did not export all three
variables there. Those exports are separate commands and need to be issued
with some separator, e.g. semicolon or newline.


>  And my execution line is:
> "*mpirun -np 4 gmx_mpi mdrun -s eq.1.tpr -v -deffnm eq.1 -pin on -ntomp 6
> -npme 1 -nb gpu -bonded gpu -pme gpu -nstlist 400*"
>

Beware that this command line is specific for one use-case presented in
your source (i.e. that very hardware and input system) and may not be fully
transferable (e.g. "-ntomp 6" or "-nstlist 400").

Cheers,
--
Szilárd


>
>  If I add "-update gpu" to this same line I have the following error:
> "
>
>
>
>
> *Inconsistency in user input:Update task on the GPU was required,but the
> following condition(s) were not satisfied:Domain decomposition without GPU
> halo exchange is not supported. With separate PME rank(s), PME must use
> direct communication.*"
>
>  Also, I'm using constraints = h-bonds in my .mdp file.
>
>  Am I doing something wrong?
>
> Thank you for your attention,
> Leandro
> ---
> Leandro Oliveira Bortot
> Postdoctoral Fellow
>  https://www.linkedin.com/in/leandro-obt/
> Laboratory of Computational Biology
> Brazilian Biosciences National Laboratory (LNBio)
> Brazilian Center for Research in Energy and Materials (CNPEM)
> Zip Code 13083-970, Campinas, São Paulo, Brazil.
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Re: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0

[Szilárd Páll]

On Sat, Apr 4, 2020 at 10:41 PM Wei-Tse Hsu  wrote:

> Dear gmx users,
> Recently I've been trying to install GROMACS 2020.1. However, I encounter a
> compilation error while using the make command. The error is as follows:
>
>
>
>
>
> */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find
> /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit
> statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2*
> From the error above, it seemed that GROMACS was unable to find library
> like libpthread.so.0 and libpthread_nonshared.a. After checking I found
> that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and
> libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/
> x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add
> the paths of the libraries for GROMACS to search for. Specifically, the
> command I was using is:
> *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd
> build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON
> -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7
> -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make
>

As Kevin noted, the separator in the prefix path should be ";".

However, it seem unnecessary to pass system libraries as custom paths to
cmake. Try first without those.

--
Szilárd



> > gmx_compile.log*
> However, it turned out that I still got the same error. I'm confused right
> now since I thought that gromacs should be able to find the files. I'm
> wondering if I missed something. Could someone please tell me what I can do
> or share some relevant experience? Any help is much appreciated!
>
> Best,
> Wei-Tse
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Re: [gmx-users] NAG N-Acetylglucosamine force field parameters

[Kenny Goossens]

Dear Javier,

The way GROMOS force fields are parameterized allows building blocks to be 
linked together and still provide a good model. You can find parameters for 
glucose in the force field (in the aminoacids.rtp file) and from there on, you 
only need to find adequate parameters for the N-acetyl group. You can try using 
the ATB web server but keep in mind to also validate the parameters that are 
generated in that case. For CHARMM, you can try using the glycan reader & 
modeler tool in the CHARMM-GUI web server, which should also provide adequate 
parameters.

With kind regards,
__
Kenneth Goossens, PhD student
Laboratory of Medicinal Chemistry (Building A - Room 2.13)
University of Antwerp - Campus Drie Eiken
Universiteitsplein 1
B-2610 Wilrijk
Belgium



Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 namens Javier Luque Di 
Salvo 
Verzonden: maandag 6 april 2020 14:14
Aan: gromacs.org_gmx-users@maillist.sys.kth.se 

Onderwerp: [gmx-users] NAG N-Acetylglucosamine force field parameters

Dear Gromacs users,

Do you know where can I search for force field parameters of
N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force
fields, my Gromacs version is 2018.3

Thanks in advance,

Javier

--



*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palerm*o*
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Re: [gmx-users] Fumbling in the dark with dihedral pulling

[Justin Lemkul]

On 4/6/20 2:33 AM, Marko Petrovic wrote:

I figure it might be helpful to see my other files so I include a link:
https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin



Your dihedral definitions are simply incorrect.

pull_coord1_groups = 1 2 2 3 3 4
pull_coord2_groups = 2 3 3 4 4 5 should be
pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -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] Bonds definition in itp files

[Justin Lemkul]

On 4/6/20 7:24 AM, Sina Omrani wrote:

Hi,
I wanted to know how we specify a bond order in our simulation? For
example, if we have a triple bond in our structure between atoms 1 and 2,
is it by length and force constants or we define 1 and 2 bonds three times
in the bond section of itp file?
What if we use a constraint on this bond? because I get better results when
I define the bond three times but haven't seen this method. is it wrong?


All interactions should be defined only once, and the parameters used 
should produce correct behavior. MM force fields have no concept of 
double or triple bonds; they only know the stiffness of the spring 
connecting the atoms. My guess is that if you had to add the bond three 
times, the force field parameters are adding together, indicating that 
the force constant is unsuitable for what you're trying to and needs to 
be refined.


-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] Protonation state of aminoacids from pdb and pdb2gmx

[Justin Lemkul]

On 4/6/20 8:10 AM, Javier Luque Di Salvo wrote:

Dear Gromacs users,

I'm aware that there might be plenty of discussions on this matter, anyway
I would like to get your advice. Which is the proper way to know the
protonation state that is generated with pdb2gmx? I have downloaded a pdb
file from the Protein Data Bank. The structure has no hydrogens, these are
added by pdb2mx.

Is this information usually available on the original pdb (like residue
names) or in the generated topology? I would like to know where to search.


pdb2gmx assigns protonation states at neutral pH assuming canonical pKa 
values for all residues. That assumption is usually good, but obviously 
is not always correct, in which case you need to manually assign the 
protonation states using command-line options.


-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] NAG N-Acetylglucosamine force field parameters

[Casalini Tommaso]

Dear Javier,

NAG is surely available in the GLYCAM library, an AMBER-based force field.



Pay attention to the scaling factors when you use GLYCAM force field, 
especially if you use it with other AMBER-based FF  (which are mutually 
compatible) in GROMACS.


Best,

Tommaso


Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 per conto di Javier Luque 
Di Salvo 
Inviato: lunedì 6 aprile 2020 14:14:39
A: gromacs.org_gmx-users@maillist.sys.kth.se
Oggetto: [gmx-users] NAG N-Acetylglucosamine force field parameters

Dear Gromacs users,

Do you know where can I search for force field parameters of
N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force
fields, my Gromacs version is 2018.3

Thanks in advance,

Javier

--



*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palerm*o*
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[gmx-users] NAG N-Acetylglucosamine force field parameters

[Javier Luque Di Salvo]

Dear Gromacs users,

Do you know where can I search for force field parameters of
N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force
fields, my Gromacs version is 2018.3

Thanks in advance,

Javier

-- 



*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palerm*o*
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[gmx-users] Protonation state of aminoacids from pdb and pdb2gmx

[Javier Luque Di Salvo]

Dear Gromacs users,

I'm aware that there might be plenty of discussions on this matter, anyway
I would like to get your advice. Which is the proper way to know the
protonation state that is generated with pdb2gmx? I have downloaded a pdb
file from the Protein Data Bank. The structure has no hydrogens, these are
added by pdb2mx.

Is this information usually available on the original pdb (like residue
names) or in the generated topology? I would like to know where to search.

Javier

-- 



*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palerm*o*
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[gmx-users] Bonds definition in itp files

[Sina Omrani]

Hi,
I wanted to know how we specify a bond order in our simulation? For
example, if we have a triple bond in our structure between atoms 1 and 2,
is it by length and force constants or we define 1 and 2 bonds three times
in the bond section of itp file?
What if we use a constraint on this bond? because I get better results when
I define the bond three times but haven't seen this method. is it wrong?

Thank you.
Sina Omrani.
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Re: [gmx-users] GROMACS 2020.1 failed to pass make check

[Paul bauer]

Hello,

you are using a plumed modified version that adds extra options to mdrun.
Our unit tests check that the output from mdrun -h stays invariant, and 
this is no longer the case once you modify the code for plumed.


You can ignore this failure in this case, but please mention in the 
future if you are using modified versions of the code.


Cheers

Paul

On 05/04/2020 21:23, Wei-Tse Hsu wrote:

Dear gmx users,
Recently I've been trying to install GROMACS 20201. After successfully
compilng GROMACS 2020.1, when executing make check command, I
encountered the following error. Specifically, one out of 56 tests failed,
which was related to Mdrun Test.WritesHelp. Looking at the error message,
I'm still not sure what it means and how I should solve this problem. I
wonder if anyone had this before that could give me some insights about how
I could solve the problem. Any help would be appreciated!

Here is the error message in the middle.





*[--] 1 test from MdrunTest[ RUN  ]
MdrunTest.WritesHelp/home/wei-tse/Documents/Software/GROMACS/gromacs-2020.1/src/testutils/refdata.cpp:867:
Failure  In item: /Help string   Actual: 'SYNOPSIS*
And here is the error message in the end.





*The following tests FAILED: 43 - MdrunTests
(Failed)CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failedCMakeFiles/Makefile2:1467: recipe for
target 'CMakeFiles/run-ctest-nophys.dir/all'
failedCMakeFiles/Makefile2:445: recipe for target
'CMakeFiles/check.dir/rule' failedMakefile:327: recipe for target 'check'
failed*

And here is the whole STDOUT message of the command printed by make *check

make_check.log*.

https://drive.google.com/file/d/1Nb2BLzA2Vl_cjS1b_M_HNk0wkrfR2WKt/view?usp=sharing

Best,
Wei-Tse



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

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Re: [gmx-users] Fumbling in the dark with dihedral pulling

[Marko Petrovic]

I figure it might be helpful to see my other files so I include a link:
https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin


With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

On 5 Apr 2020, at 23:09, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 4/5/20 5:05 PM, Marko Petrovic wrote:
Hello.

I've been trying to do coordinate pulling of dihedral angles of an alanine 
dipeptide in vacuum and used the umbrella sampling tutorial as a starting 
point. I'm trying to generate initial configurations for later runs, but the 
mdrun ends in a segmentation fault with error messages like:

Step 15707, time 31.414 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025328, max 0.098100 (between atoms 11 and 13)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  7  8   90.40.1006   0.1054  0.0997
 11 13   90.20.1110   0.1220  0.

Step 15708, time 31.416 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 52572448.00, max 238546496.00 (between atoms 7 and 8)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  7  8  109.30.1054 23783084.  0.0997
  9 11  119.50.1543 1995948.6250  0.1538
 11 12  162.60.1127 1995948.6250  0.
 11 13  115.60.1220 1995948.5000  0.
 11 14  112.70.1124 1995948.6250  0.
Wrote pdb files with previous and current coordinates
Segmentation fault: 11

Perhaps the seg fault is not related to the warnings at all but as I am not 
certain what they mean and do think they are enough to cause some problems 
anyway I would like to understand them in general and also know what columns 
previous and current are saying.

They refer to bond lengths, what the length was at the previous step and what 
it is now, compared to what the reference value should be. Your values indicate 
catastrophic distortion of the structure.

As the original tutorial was done for a water solution and mine is conducted in 
vacuum I am guessing my modifications to the .mdp files are not completely 
updated so any tips on that woul also be helpful.

There's no way to provide any useful advice without you posting your .mdp file. 
Note that the umbrella sampling tutorial has basically no relevance to anything 
you're doing because enforced dihedral rotation didn't exist when I wrote it :)

-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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