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!
> >> > > >
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> >> > > > * 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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> >> > >
> >> >
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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
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> > > posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] gromacs instillation

[Ali Ahmed]

Dear Rahul,
Thank you for your answer. Yes, I did remove the old version and all its
dependencies.
Usually, I use these commands for installation

mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

This time I got this error and tried several options with no luck


Thanks
Ali



On Wed, Apr 10, 2019 at 10:55 PM RAHUL SURESH 
wrote:

> Hi
>
> On Thu 11 Apr, 2019, 8:39 AM 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.
>
> This means gromacs is not installed in the source directory. Simple., You
> will know where you have the gromacs executable. Just give that address in
> source. Or better set it in bash so you needn't go for source everytime.
>
> > You can install it by typing:  sudo apt install gromacs. When I
> > did it, the version became 5.1.2.
> >
>
> That's wrong procedure. If you want 2019 version then you got to start
> from scratch. Delete all you preexisting gromacs file and reinstall 2019
> Ver. Don't use apt-get.
>
> >
> > Any idea how to solve it!
> >
> > Thank you
> > Ali
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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[gmx-users] gromacs instillation

[Ali Ahmed]

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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[gmx-users] High potential energy

[Ali Ahmed]

Hello GMX users
I'm simulating a complex system. I started with energy minimization step
which went fine then followed by a short NPT for equilibration then
followed by energy minimization for more minimization and its output as
below
Steepest Descents converged to Fmax < 10 in 3783 steps
Potential Energy  = -3.0612996e+04
Maximum force =  9.8396473e+00 on atom 3209
Norm of force =  1.0086957e+00

However, when I started NVT production, I see the potential of the system
goes up to a positive value
Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  Improper Dih.  LJ-14
7.61233e+048.43296e+022.83000e+042.89344e+026.94750e+04
 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
   -1.58903e+04   -8.17942e+04   -1.07861e+045.24188e+035.14340e+03
  PotentialKinetic En.   Total Energy  Conserved En.Temperature
7.69455e+041.16251e+051.93197e+05   -7.02956e+043.00338e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -3.58345e+022.99966e+026.24109e-05
I don't know what happened and why the potential goes up. Should I worry
about this?

Thanks
ِAli
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Re: [gmx-users] Large system

[Ali Ahmed]

Sir
I have done a simulation of 106000 atoms and there was no problem.
Check your number of molecules in your topology and inspect your input file
you will find something wrong. The error says the number of atoms is not
the same in topology and your input.
I suggest using *.gro  rather than pdb which make it easier to check and
inspect the number of atoms and residues and check the top of gro file this
number represents the total number of atoms in your system.

Best

On Wed, Jan 2, 2019 at 12:47 AM Anuj Ray  wrote:

> Sir,
>
> Since the array size of .gro/.pdb file for atom number is not greater than
> 5 digits, that's why if my system has >= 10 atoms then, it shows that
> no. of coordinates mismatch in .gro and .top file. Although the file
> corrected_wat_DMPC_18_32.pdb has 153216 coordinates, i get the following
> error.
>
> Command line:
>   gmx grompp -f minim.mdp -c corrected_wat_DMPC_18_32.pdb -p dmpctopol.top
> -o em.tpr
>
> Fatal error:
> number of coordinates in coordinate file (corrected_wat_DMPC_18_32.pdb,
> 9)
>  does not match topology (dmpctopol.top, 153216)
>
>
>
>
>
>
>
>
> On Wed, Jan 2, 2019 at 12:18 AM  wrote:
>
> > [image: Boxbe]  This message is eligible
> > for Automatic Cleanup! (pbusc...@q.com) Add cleanup rule
> > <
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3DHrOF%252BjTOvp0Cf6CNxnGnxFFovz45l3r%252BVv684FrcTxU%253D%26token%3DuwjKuuWXMIOgCqLDQJs%252FZv5SDAdb6Oo%252Bo7D3WuJIGjbMuUsyDiNs2k0G1JlQwHvZp6LfurXxmiQ2kSU4i5Ul%252BRqdZmtveskcPfgAyNak2ctwu4ZCYxZu5xgUXI7o8%252F1Hw%252Fhsq6MhOVk%253D_serial=46674948998_rand=1281816478_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001
> >
> > | More info
> > <
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=46674948998_rand=1281816478_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001
> >
> > As suggested,  compare the number of molecules/atoms implied in your top
> > file against that in your gro/pdb file.  This is one aspect of Gromacs
> that
> > it never gets wrong.
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >  On Behalf Of Bratin
> > Kumar Das
> > Sent: Tuesday, January 01, 2019 5:22 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Large system
> >
> > There must be something wrong in your pdb or gro file. Give the proper
> > error
> > message. They way you told your problem..no one can understand.
> >
> > On 01-Jan-2019 11:41 AM, "Anuj Ray"  wrote:
> >
> > Respected Sir
> >
> > I am trying to prepare a minimization input file (.tpr) for a system
> having
> > 153216 atoms but the grompp command is reading only upto 9 atoms.
> What
> > is the procedure to prepare the input for such system?
> >
> > Regards
> > Anuj
> > --
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Re: [gmx-users] pdb generator

[Ali Ahmed]

You should know how many atoms in each residue then how many residues of
XXX you have then you can see.
Suggestion, if possible use sperate pdb files then use solvation option to
produce your system .gro  or pdb. This will help you in editing each pdb
then get your correct gromacs input files.
Best

On Tue, Nov 13, 2018 at 9:35 AM Momin Ahmad  wrote:

> Hi Ali,
>
> thanks for you help. How can you distinguish between a C atom from
> residue XXX and another C atom from residue YYY when there are about
> 2000 atoms in the file. Did you write a script for that? If there doesnt
> exist a tool with a GUI to solve this then i will have to write my own
> builder.
>
> Cheers
>
> Momin
>
> Am 13.11.18 um 16:31 schrieb Ali Ahmed:
> > well if you use Linux then you can use GVim to do highlight and do simple
> > changes on one type only then use find and replace option. That what I do
> > when I have more than one type. It needs one hour practice then you will
> be
> > ok. Or you can write a script for such things.
> > Best
> >
> > On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad  wrote:
> >
> >> Hi Ali,
> >>
> >> my problem is that there is not only one molecule but two different
> >> molecules which build up a crystaline structure. For example i have 10
> >> XXX and 100 YYY in the .pdb file.
> >>
> >> Cheers
> >>
> >> Momin
> >>
> >> Am 13.11.18 um 16:12 schrieb Ali Ahmed:
> >>> Hi,
> >>> I use Avogadro and it is easy to change LIG to anything you want. I
> just
> >>> use find and replace option which takes less than a minute.
> >>> Best
> >>> Ali
> >>>
> >>> On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad 
> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> is there a tool where i can use for example a .cif file (or .xyz) file
> >>>> to generate a .pdb file with correct classification? For example
> >>>> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> >>>> also another tool which can be used to generate large scale crystal
> >>>> structures with building blocks as input?
> >>>>
> >>>>
> >>>> Cheers
> >>>>
> >>>> Momin
> >>>>
> >>>> --
> >>>> Momin Ahmad
> >>>>
> >>>> Karlsruhe Institute of Technology (KIT)
> >>>> Steinbuch Centre for Computing (SCC)
> >>>> Hermann-von-Helmholtz-Platz 1
> >>>> 76344 Eggenstein-Leopoldshafen
> >>>> Phone: +49 721 608-24286
> >>>> E-Mail: momin.ah...@kit.edu
> >>>>
> >>>> --
> >>>> 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.
> >>>>
> >> --
> >> Momin Ahmad
> >>
> >> Karlsruhe Institute of Technology (KIT)
> >> Steinbuch Centre for Computing (SCC)
> >> Hermann-von-Helmholtz-Platz 1
> >> 76344 Eggenstein-Leopoldshafen
> >> Phone: +49 721 608-24286
> >> E-Mail: momin.ah...@kit.edu
> >>
> >> --
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> >>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
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Re: [gmx-users] pdb generator

[Ali Ahmed]

well if you use Linux then you can use GVim to do highlight and do simple
changes on one type only then use find and replace option. That what I do
when I have more than one type. It needs one hour practice then you will be
ok. Or you can write a script for such things.
Best

On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad  wrote:

> Hi Ali,
>
> my problem is that there is not only one molecule but two different
> molecules which build up a crystaline structure. For example i have 10
> XXX and 100 YYY in the .pdb file.
>
> Cheers
>
> Momin
>
> Am 13.11.18 um 16:12 schrieb Ali Ahmed:
> > Hi,
> > I use Avogadro and it is easy to change LIG to anything you want. I just
> > use find and replace option which takes less than a minute.
> > Best
> > Ali
> >
> > On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad  wrote:
> >
> >> Hi,
> >>
> >> is there a tool where i can use for example a .cif file (or .xyz) file
> >> to generate a .pdb file with correct classification? For example
> >> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> >> also another tool which can be used to generate large scale crystal
> >> structures with building blocks as input?
> >>
> >>
> >> Cheers
> >>
> >> Momin
> >>
> >> --
> >> Momin Ahmad
> >>
> >> Karlsruhe Institute of Technology (KIT)
> >> Steinbuch Centre for Computing (SCC)
> >> Hermann-von-Helmholtz-Platz 1
> >> 76344 Eggenstein-Leopoldshafen
> >> Phone: +49 721 608-24286
> >> E-Mail: momin.ah...@kit.edu
> >>
> >> --
> >> 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.
> >>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
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Re: [gmx-users] pdb generator

[Ali Ahmed]

Hi,
I use Avogadro and it is easy to change LIG to anything you want. I just
use find and replace option which takes less than a minute.
Best
Ali

On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad  wrote:

> Hi,
>
> is there a tool where i can use for example a .cif file (or .xyz) file
> to generate a .pdb file with correct classification? For example
> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> also another tool which can be used to generate large scale crystal
> structures with building blocks as input?
>
>
> Cheers
>
> Momin
>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
> --
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> * Please search the archive at
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Re: [gmx-users] TOPOLOGY AND GRO FILE ATOMS NAME MISMATCH

[Ali Ahmed]

Hi
I believe gromacs uses atom names from topology if they are not matching.
Check atoms in PDB and compare them with topology then you will find what
is missing or the differences
Ali

On Sun, Nov 4, 2018 at 7:05 AM K. Subashini  wrote:

> Hi gromacs users,
>
> For an organic molecule,  the topology file was built using opls
> forcefield was obtained.
>
> Using gmx insert command, the gro file containing 150 molecules of the
> same organic compound placed in a box was obtained.
>
> Now the topology and gro file have non-matching atom names.
>
>
> How to fix the error?
>
> Thanks,
> Subashini.K
>
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Re: [gmx-users] topol file inaccessible

[Ali Ahmed]

hi
check your commands from misspelling

On Sat, Jul 21, 2018 at 10:08 AM, Raag Saluja  wrote:

> Hi!
> I'm simulating a heterodimer. The simulation goes really smoothly till the
> MD production step where I get an error saying the topol file is
> inaccessible. Can you please help?
>
> Thank you in advance and regards,
> Raag
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Re: [gmx-users] Trouble running simulations with Nitrogen

[Ali Ahmed]

Hi
Try this

http://erg.biophys.msu.ru/tpp/

Best

On Thu, Jul 19, 2018 at 10:54 PM, Joshua Cummings <
joshua.cummi...@uon.edu.au> wrote:

> Hi Everyone,
>
>
> I'm currently trying to run some simulations that involve the absorption
> of N2 into a liquid solvent. I'm having some difficulty in generating the
> topology for N2. For reference, the pdb file I have for N2 is as follows:
>
>
> HETATM1  N6B HDZ 0   0.000   0.000   0.553  1.00  0.00
>N
> HETATM2  N6A HDZ 0   0.000   0.000  -0.553  1.00  0.00
>N
> CONECT12
> CONECT21
> END
>
>
> When I try to generate the .itp file and topology via pdb2gmx (OPLS),
> gromacs doesn't recognise the residue. I've tried using both the LigParGen
> server and the PRODRG to generate the topology, but neither work. PRODRG
> generates an error saying it does not deal with mono/di-atomic molecules
> and LigParGen won't recognise N2 at all.
>
>
> I haven't had any trouble generating topologies for other small gas
> molecules such as CH4, am I missing something here or are OPLS parameters
> not possible for N2? Should I use some other forcefield for N2?
>
>
> Thanks in advance everyone,
>
>
> JOSHUA Cummings
>
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Re: [gmx-users] Magnetic field in GROMACS

[Ali Ahmed]

Hello,
I looked for that before and I tried updating the electric field code as
both of them are related to Lorentz force. Unfortunately, I failed because
there are different codes need to be updated.
It would be amazing if the developers participate in this code.
Thanks
Ali

On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel 
wrote:

> Den 2018-06-20 kl. 10:20, skrev Alex:
>
>> David,
>>
>> I can think of many realistic cases when looking at the effects of
>> magnetic fields in MD would be of interest, just not in what Gromacs is
>> normally used for.
>>
>> It's just a completely different animal in terms of what causes those
>> effects and Lorentz force applied to point charges would likely be a very
>> bad approximation. But in general, an implementation of self-consistent
>> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.
>>
>
> Feel free to open a redmine issue to discuss it there.
> We have an implementation of electric fields that can be used as a
> template.
>
>
>> Alex
>>
>>
>>
>>> Magnetic fields are typically very weak such that they are negligable in
>>> realistic cases. This is why nobody bothered to implement it.
>>>
>>>
>>
>
> --
> 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] md simulation of oil hydrocarbon

[Ali Ahmed]

for liquids use oplsaa

On Mon, May 28, 2018 at 12:23 PM, Atila Petrosian  wrote:

> Hi all,
>
> I want to do md simulation of oil hydrocarbon?
>
> Is there appropriate force field for these hydrocarbons in gromacs?
>
> What I see in gromacs force fields only was related to aminoacids and
> nucleotides.
>
> What is your suggestion for md simulation of oil hydrocarbon?
>
> Best,
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Re: [gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Hi Mark,
Yes, I used that and I have no idea what happened.
First I removed old version then downloaded 2018 version and used these
commands:

tar xfz gromacs-2018.1.tar.gz
cd gromacs-2018.1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Thanks

On Sun, May 27, 2018 at 3:50 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Some other version of GROMACS is being found. Follow the official
> instructions at
> http://manual.gromacs.org/documentation/current/install-
> guide/index.html#getting-access-to-gromacs-after-installation
>
> Mark
>
> On Sun, May 27, 2018, 10:31 Ali Ahmed <aa5635...@gmail.com> wrote:
>
> > Hi Kevin,
> > Yes, I had it, but I removed GROMACS 5.1.2 before trying to install 2018
> > version.
> > Thanks
> > Ali
> >
> > On Sun, May 27, 2018 at 12:05 AM, Kevin Boyd <kevin.b...@uconn.edu>
> wrote:
> >
> > > Hi,
> > >
> > > Did you have a previous install of gromacs 5.1.2? If so, it’s
> potentially
> > > a case of you having two installations of gromacs, and the first one
> > found
> > > by your os when you try to run gmx [command] is 5.1.
> > >
> > > Kevin
> > >
> > > > On May 27, 2018, at 12:10 AM, Ali Ahmed <aa5635...@gmail.com> wrote:
> > > >
> > > > Dear Soham,
> > > > I followed website instructions. I could not find instructions by
> > Sridhar
> > > > Manchu for 2018 version.
> > > > Thanks
> > > >
> > > >> On Sat, May 26, 2018 at 10:54 PM, Soham Sarkar <soham9...@gmail.com
> >
> > > wrote:
> > > >>
> > > >> Follow installation by Sridhar Manchu
> > > >>
> > > >>> On Sun, 27 May 2018, 4:23 am Ali Ahmed, <aa5635...@gmail.com>
> wrote:
> > > >>>
> > > >>> Hello GROMACS users,
> > > >>>
> > > >>> I'm trying to install GROMACS 2018 on my laptop. I followed the
> > > >>> instructions on GROMACS website and everything looks fine.
> > > >>> But when I check the version. it says :  :-) GROMACS - gmx, VERSION
> > > 5.1.2
> > > >>> (-: .
> > > >>> Please, can anyone tell me how to install 2018 version? because I
> > need
> > > to
> > > >>> use electric field options
> > > >>>
> > > >>> 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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> > > >>>
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> > or
> > > >>> send a mail to gmx-users-requ...@gromacs.org.
> > > >> --
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Re: [gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Hi Kevin,
Yes, I had it, but I removed GROMACS 5.1.2 before trying to install 2018
version.
Thanks
Ali

On Sun, May 27, 2018 at 12:05 AM, Kevin Boyd <kevin.b...@uconn.edu> wrote:

> Hi,
>
> Did you have a previous install of gromacs 5.1.2? If so, it’s potentially
> a case of you having two installations of gromacs, and the first one found
> by your os when you try to run gmx [command] is 5.1.
>
> Kevin
>
> > On May 27, 2018, at 12:10 AM, Ali Ahmed <aa5635...@gmail.com> wrote:
> >
> > Dear Soham,
> > I followed website instructions. I could not find instructions by Sridhar
> > Manchu for 2018 version.
> > Thanks
> >
> >> On Sat, May 26, 2018 at 10:54 PM, Soham Sarkar <soham9...@gmail.com>
> wrote:
> >>
> >> Follow installation by Sridhar Manchu
> >>
> >>> On Sun, 27 May 2018, 4:23 am Ali Ahmed, <aa5635...@gmail.com> wrote:
> >>>
> >>> Hello GROMACS users,
> >>>
> >>> I'm trying to install GROMACS 2018 on my laptop. I followed the
> >>> instructions on GROMACS website and everything looks fine.
> >>> But when I check the version. it says :  :-) GROMACS - gmx, VERSION
> 5.1.2
> >>> (-: .
> >>> Please, can anyone tell me how to install 2018 version? because I need
> to
> >>> use electric field options
> >>>
> >>> 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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> >>>
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> >>> send a mail to gmx-users-requ...@gromacs.org.
> >> --
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Re: [gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Dear Soham,
I followed website instructions. I could not find instructions by Sridhar
Manchu for 2018 version.
Thanks

On Sat, May 26, 2018 at 10:54 PM, Soham Sarkar <soham9...@gmail.com> wrote:

> Follow installation by Sridhar Manchu
>
> On Sun, 27 May 2018, 4:23 am Ali Ahmed, <aa5635...@gmail.com> wrote:
>
> > Hello GROMACS users,
> >
> > I'm trying to install GROMACS 2018 on my laptop. I followed the
> > instructions on GROMACS website and everything looks fine.
> > But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
> > (-: .
> > Please, can anyone tell me how to install 2018 version? because I need to
> > use electric field options
> >
> > 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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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Hello Benson,
Yes, I did.

On Sat, May 26, 2018 at 9:49 PM, Benson Muite <benson.mu...@ut.ee> wrote:

>
>
> On 05/27/2018 01:53 AM, Ali Ahmed wrote:
>
>> Hello GROMACS users,
>>
>> I'm trying to install GROMACS 2018 on my laptop. I followed the
>> instructions on GROMACS website and everything looks fine.
>> But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
>> (-: .
>> Please, can anyone tell me how to install 2018 version? because I need to
>> use electric field options
>>
>> Thank you
>> Ali
>>
>>
> Did you download a release version from:
> http://manual.gromacs.org/documentation/
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[gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Hello GROMACS users,

I'm trying to install GROMACS 2018 on my laptop. I followed the
instructions on GROMACS website and everything looks fine.
But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
(-: .
Please, can anyone tell me how to install 2018 version? because I need to
use electric field options

Thank you
Ali
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Re: [gmx-users] viscosity calculation using g_energy

[Ali Ahmed]

Hello David,
Thank you for your reply,
After 5 ns of equilibrium, I run the simulation for 10 ns of heptane, but
in the results of Einstein viscosity, I got only 5 ns.
There are two files evisco.xvg and viscosity .xvg. In the first one, there
are different columns but I think the last one is the viscosity of Einstein
relation. The second one is the viscosity that I'm looking for.
The results are far from the experimental results. Heptane experimental
viscosity at 300 k is 0.376 cp but my results were so far as shown in the
link below. Bulk viscosity goes to negative values which is incorrect.
I'm confused a bit about the results and calculations.

https://ibb.co/cb5fjx

Thanks in advance


On Sun, Apr 8, 2018 at 3:27 AM, David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

> Den 2018-04-06 kl. 01:55, skrev Ali Ahmed:
>
>> Hello David,
>> I have the same problem
>> I run the simulation for 10 ns and I saved energies every 1 ps but the
>> results were far and the curves go to negative values.
>> Please, do have an idea how to get accurate results?
>> Thank you
>> Ali
>>
>
> You give no information on numbers or what the einstein viscosity curve
> look like.
>
>
>
>>
>>
>> On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel <sp...@xray.bmc.uu.se
>> >
>> wrote:
>>
>> Den 2018-04-05 kl. 09:19, skrev Jo:
>>>
>>> Hello,
>>>>
>>>> I would like to calculate bulk and shear viscosity on gromacs using
>>>> g_energy.  I have read a number of other emails about this topic but
>>>> there
>>>> still seems to be no conclusive answer to how to use this tool.  I use
>>>> the
>>>> following command:
>>>>
>>>> gmx energy -f  prod_500.edr -vis viscosity.xvg
>>>>
>>>>
>>> The einstein viscosity is usually more accurate. How long is your
>>> simulation and how often do you save the energies?
>>>
>>>
>>>  From this, a file called 'viscosity.xvg' is produced with data on time
>>>>
>>>>>
>>>>> (ps), shear viscosity, and bulk viscosity.  However, these values
>>>> fluctuate
>>>> wildly and are off from the correct viscosity for this model (SPCE) by
>>>> at
>>>> least an order of magnitude.  I know the simulation trajectory is
>>>> correct
>>>> as I have matched potential energy, density, and diffusion coefficition
>>>> for
>>>> these runs with literature.  However, the viscosity numbers are far off
>>>> from the expected values.
>>>>
>>>> Any suggesions on what I can try?  I assume there must be a way to do it
>>>> by
>>>> hand via the pressure tensors.  Can someone directly me to how I can
>>>> practically take the pressure tensors to calculate via Green-Kubo method
>>>> the viscosity?
>>>>
>>>> Thanks,
>>>>
>>>> Shuwen
>>>>
>>>>
>>>>
>>> --
>>> 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
>>>
>>> --
>>> Gromacs Users mailing list
>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>
> --
> 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] viscosity calculation using g_energy

[Ali Ahmed]

Hello David,
I have the same problem
I run the simulation for 10 ns and I saved energies every 1 ps but the
results were far and the curves go to negative values.
Please, do have an idea how to get accurate results?
Thank you
Ali



On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel 
wrote:

> Den 2018-04-05 kl. 09:19, skrev Jo:
>
>> Hello,
>>
>> I would like to calculate bulk and shear viscosity on gromacs using
>> g_energy.  I have read a number of other emails about this topic but there
>> still seems to be no conclusive answer to how to use this tool.  I use the
>> following command:
>>
>> gmx energy -f  prod_500.edr -vis viscosity.xvg
>>
>
> The einstein viscosity is usually more accurate. How long is your
> simulation and how often do you save the energies?
>
>
>> From this, a file called 'viscosity.xvg' is produced with data on time
>>>
>> (ps), shear viscosity, and bulk viscosity.  However, these values
>> fluctuate
>> wildly and are off from the correct viscosity for this model (SPCE) by at
>> least an order of magnitude.  I know the simulation trajectory is correct
>> as I have matched potential energy, density, and diffusion coefficition
>> for
>> these runs with literature.  However, the viscosity numbers are far off
>> from the expected values.
>>
>> Any suggesions on what I can try?  I assume there must be a way to do it
>> by
>> hand via the pressure tensors.  Can someone directly me to how I can
>> practically take the pressure tensors to calculate via Green-Kubo method
>> the viscosity?
>>
>> Thanks,
>>
>> Shuwen
>>
>>
>
> --
> 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
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] Deleting a folder

[Ali Ahmed]

Hi Justin,
Thanks for your answer. So, how can I update a code in GROMACS?
Best
Ali

On Tue, Feb 27, 2018 at 5:25 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 2/27/18 6:23 PM, Ali Ahmed wrote:
>
>> Hello GROMACS users,
>>
>> I'm sorry for the crazy things I did.
>> I was trying to update electric filed code for magnetic filed
>> implementation by adding the cross product term to the force calculation
>> equation. unfortunately, I failed and deleted the mdlib folder (GROMACS
>> 5.1.2).
>> The surprising thing is that GROMAS still applies electric filed.
>> My question is, how does GROMACS apply electric field while the code is
>> deleted?
>>
>
> Deleting source code has no effect on software that's already installed.
> If you try to install again, then your compilation would fail due to
> missing files.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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[gmx-users] Deleting a folder

[Ali Ahmed]

Hello GROMACS users,

I'm sorry for the crazy things I did.
I was trying to update electric filed code for magnetic filed
implementation by adding the cross product term to the force calculation
equation. unfortunately, I failed and deleted the mdlib folder (GROMACS
5.1.2).
The surprising thing is that GROMAS still applies electric filed.
My question is, how does GROMACS apply electric field while the code is
deleted?

Best
Ali
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Thank you
I'm trying to update it for external magnetic filed applications

On Sun, Feb 18, 2018 at 12:57 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Suggestion, get the git version of gromacs and use
>
>  git grep -i -G"electric field"
>
> src/gromacs/applied-forces
>
> Mark
>
> On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed <aa5635...@gmail.com> wrote:
>
> > Dear Mark,
> > I could not find the electric field calculation code. In 2016 version,
> the
> > code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
> > Is it elsewhere? can you tell me, please?
> > Thanks
> >
> > On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed <aa5635...@gmail.com> wrote:
> >
> > > Dear Mark,
> > > Thank you. this is good I will study it.
> > >
> > >
> > > On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> See section 6.7 of the 2018 reference manual for what is supported.
> > >>
> > >> MArk
> > >>
> > >> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed <aa5635...@gmail.com>
> wrote:
> > >>
> > >> > Hello GROMACS users
> > >> > I have looked through GROMACS user manual to understand the theory
> > >> behind
> > >> > applying external electric field but I did not find any description.
> > >> Also,
> > >> > I looked at the source code in  sim_util.cpp file but found only the
> > >> > time-dependent electric field.
> > >> > My question does GROMACS consider Lorentz force for applying
> external
> > >> > electric field or using another theory?
> > >> > Thanks
> > >> > 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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> or
> > >> > send a mail to gmx-users-requ...@gromacs.org.
> > >> >
> > >> --
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> > >>
> > >
> > >
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Re: [gmx-users] PROBLEM IN COORDINATES

[Ali Ahmed]

check your sol.gro if you have molecules more or less than given in your
topology
Best

On Sun, Feb 18, 2018 at 12:34 PM, neelam wafa  wrote:

> Dear gmx users,
>
> I am doing the tutorial of protein ligand simmulation given at
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com
> .
> when I give following command, I get an error.
>
> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
> the error says the number of coordinates in the sol.gro file and
> topol.top file does not match. How to fix it.
>
> Help me out please.
>
> Thanks in advance.
>
> Regards
> --
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Dear Mark,
I could not find the electric field calculation code. In 2016 version, the
code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
Is it elsewhere? can you tell me, please?
Thanks

On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed <aa5635...@gmail.com> wrote:

> Dear Mark,
> Thank you. this is good I will study it.
>
>
> On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
>> Hi,
>>
>> See section 6.7 of the 2018 reference manual for what is supported.
>>
>> MArk
>>
>> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed <aa5635...@gmail.com> wrote:
>>
>> > Hello GROMACS users
>> > I have looked through GROMACS user manual to understand the theory
>> behind
>> > applying external electric field but I did not find any description.
>> Also,
>> > I looked at the source code in  sim_util.cpp file but found only the
>> > time-dependent electric field.
>> > My question does GROMACS consider Lorentz force for applying external
>> > electric field or using another theory?
>> > Thanks
>> > 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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>> >
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>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
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>>
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>>
>
>
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Dear Mark,
Thank you. this is good I will study it.


On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> See section 6.7 of the 2018 reference manual for what is supported.
>
> MArk
>
> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed <aa5635...@gmail.com> wrote:
>
> > Hello GROMACS users
> > I have looked through GROMACS user manual to understand the theory behind
> > applying external electric field but I did not find any description.
> Also,
> > I looked at the source code in  sim_util.cpp file but found only the
> > time-dependent electric field.
> > My question does GROMACS consider Lorentz force for applying external
> > electric field or using another theory?
> > Thanks
> > 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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[gmx-users] Electric Field

[Ali Ahmed]

Hello GROMACS users
I have looked through GROMACS user manual to understand the theory behind
applying external electric field but I did not find any description.  Also,
I looked at the source code in  sim_util.cpp file but found only the
time-dependent electric field.
My question does GROMACS consider Lorentz force for applying external
electric field or using another theory?
Thanks
Ali
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Re: [gmx-users] GROMACS 2018 second beta

[Ali Ahmed]

Dear Mark,
Thank you for all of your efforts.
I wish you added an option for applying external magnetic field in this
version.
Thanks
Ali

On Mon, Dec 11, 2017 at 8:54 PM, Mark Abraham 
wrote:

> Hi GROMACS users,
>
> The second beta release of GROMACS 2018 is available! (We know it's only
> 2017 right now, but by the time we make the real release it will be almost
> 2018, so that seems like a good idea!)
>
> We are making this available to you to get an early taste of how GROMACS
> 2018 will look and work, and most importantly to get feedback from you
> about how well things work. While we try our hardest to keep the quality of
> GROMACS as high as possible, we’re human, we overlook things while doing
> other things, and we need your many pairs of eyes to help build a tool that
> we can all use to do good science! We really need you to test your kinds of
> simulation on your hardware, both for correctness and performance. This is
> particularly important if you are using "interesting" hardware or
> compilers, because we can't test all of them!
>
> We've fixed a number of minor issues that users and developers identified -
> please do try out the new version to see if you agree that things have been
> fixed where we think they have. No major issues have been identified, which
> is very good news. See the release notes for details.
>
> Please do not use this version for doing science you plan to publish - it
> needs more testing before it’s reliable enough for that. Similarly, please
> don’t use this version as a base for a project that bundles or forks
> GROMACS.
>
> What new things can you expect? (See the release notes for more details.)
> * support for PME running on a GPU
> * improvements for performance of the short-ranged scheme, particularly on
> GPUs, through optimizing the pair-list handling
> * support for the AWH adaptive biasing scheme
> * new simulation quality checks on physical properties of the integrator
> * CPU-side enhancements from adding some or better SIMD support to several
> computations
> * more reporting of conserved quantities for integrators
>
> Just so you know, a fair bit of the work done since 2016 has been
> re-organizational, rather than new features or faster performance.
>
> There’s lots of other new things, and a few old things removed - please see
> the link to the release notes. All the content of GROMACS 2016.4 (plus
> several yet-to-be-released bug fixes) is present, apart from features that
> have been removed.
>
> If all goes to plan, we hope to ship the final 2018 release in time for the
> New Year, but that relies on people joining in and helping us test! We hope
> you will consider making that contribution, so that we can continue to
> deliver high-quality free simulation software that will be useful to you on
> January 1.
>
> You can find the code, manual, release notes, installation instructions and
> testsuite at the links below.
>
> Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018-beta2.tar.gz
> Documentation: http://manual.gromacs.org/documentation/2018-beta2/
> index.html
> (includes install guide, user guide, reference manual)
> Release Notes:
> http://manual.gromacs.org/documentation/2018-beta2/ReleaseNotes/index.html
> Test Suite:
> http://gerrit.gromacs.org/download/regressiontests-2018-beta2.tar.gz
>
> Happy testing!
>
> Mark Abraham
> GROMACS Development Manager
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[gmx-users] Simulation on multi nodes performance

[Ali Ahmed]

Hello GMX users

I'm trying to do simulations on multi nodes so I used  8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.

I used these commands:

---

load apps/gromacs-2016

load apps/openmpi-2.1.1

gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr

mpirun -np 128 mdrun_mpi -v -deffnm EMZ



I'm kind of confused about the right commands

Any comment will be helpful

Thanks in advance

Ali
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[gmx-users] Restarting crashed simulation

[Ali Ahmed]

Hello GROMACS users
My MD simulation was crashed then I restarted the simulation from the point
when the point was written using this command on 64 processors: mpirun -np
64  mdrun_mpi -s md.tpr -cpi stat.cpt

After few days I got nothing in the folder usch as output.gro and I got the
following
___
Command line:
  mdrun_mpi -s md.tpr -cpi stat.cpt

Warning: No checkpoint file found with -cpi option. Assuming this is a new
run.


Back Off! I just backed up md.log to ./#md.log.2#

Running on 4 nodes with total 64 cores, 64 logical cores
  Cores per node:   16
  Logical cores per node:   16
Hardware detected on host compute-2-27.local (the node of MPI rank 0):
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256

  Hardware topology: Basic

Reading file md.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.003

Will use 48 particle-particle and 16 PME only ranks
This is a guess, check the performance at the end of the log file
Using 64 MPI processes
Using 1 OpenMP thread per MPI process

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
WARNING: This run will generate roughly 50657 Mb of data

starting mdrun 'Molecular Dynamics'
2500 steps,  5.0 ps.

step 888000 Turning on dynamic load balancing, because the performance loss
due to load imbalance is 8.7 %.
step 930400 Turning off dynamic load balancing, because it is degrading
performance.
step 1328000 Turning on dynamic load balancing, because the performance
loss due to load imbalance is 3.4 %.
step 1328800 Turning off dynamic load balancing, because it is degrading
performance.
step 1336000 Turning on dynamic load balancing, because the performance
loss due to load imbalance is 3.4 %.
step 1338400 Turning off dynamic load balancing, because it is degrading
performance.
step 134 Will no longer try dynamic load balancing, as it degraded
performance.
Writing final coordinates.
 Average load imbalance: 13.2 %
 Part of the total run time spent waiting due to load imbalance: 7.5 %
 Average PME mesh/force load: 1.077
 Part of the total run time spent waiting due to PP/PME imbalance: 4.1 %

NOTE: 7.5 % of the available CPU time was lost due to load imbalance
  in the domain decomposition.
  You might want to use dynamic load balancing (option -dlb.)


   Core t (s)   Wall t (s)(%)
   Time: 26331875.601   411435.556 6400.0
 4d18h17:15
 (ns/day)(hour/ns)
Performance:   10.5002.286
_

Any advise or suggestion will be helpful.

Thanks in advance
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Re: [gmx-users] Number of coordinates in .gro file does not match topology

[Ali Ahmed]

Hi,

Check your box size,I had a same problem. I used a larger box then the
problem solved.

Best
Ali

On Mon, Oct 30, 2017 at 6:29 PM, Mark Abraham 
wrote:

> Hi,
>
> How big is the system before and after? Gro format used fixed columns, so
> can sometimes struggle with large systems. Try using .g96 as the output
> file extension
>
> Mark
>
> On Mon, 30 Oct 2017 17:29  wrote:
>
> > Checked the file again. It is the one that gets generated after the
> > solvation command is run.
> >
> > Sent from my iPhone
> >
> > > On 30-Oct-2017, at 9:39 PM, Mark Abraham 
> > wrote:
> > >
> > > Hi,
> > >
> > > The most likely scenario is that you are looking at a gro file that is
> > not
> > > the one that was written by the solvation tool.
> > >
> > > Mark
> > >
> > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti <
> > > smritiaishwary...@gmail.com> wrote:
> > >
> > >> Hi!
> > >>
> > >> I'm trying to solvate a system of a CNT and a protein molecule. My
> > updated
> > >> topology file shows 106275 new solvent molecules added but the .gro
> file
> > >> has only coordinates for 6197 new molecules. I'm using SPC model for
> > >> solvating, Please help.
> > >>
> > >> Regards,
> > >> Aishwarya Smriti
> > >> Senior Undergraduate
> > >> Chemical Engineering
> > >> Indian Institute of Technology, Delhi
> > >> --
> > >> Gromacs Users mailing list
> > >>
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> > >> posting!
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> > >>
> > > --
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> > posting!
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[gmx-users] GROMACS on a cluster

[Ali Ahmed]

Dear GROMACS users

I need to work on a cluster which has 30 nodes, each has 8 processors

I need to work on 8 nodes (64 processors). For mdrun I used this command:

 mpirun -np 64 gmx_mpi mdrun ..

but the simulation failed to start and here is the error

--
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
  line parameter option (remember that mpirun interprets the first
  unrecognized command line token as the executable).

Node:   login-1
Executable: gmx_mpi
--
16 total processes failed to start

I could not figur this error.
Any suggestions will be appreciated

Thanks in advance
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Dear all,
Thank you for helping me. All I get from grompp is this
--

gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file grompp.mdp]:
  The group cutoff scheme is deprecated since GROMACS 5.0 and will be
  removed in a future release when all interaction forms are supported for
  the verlet scheme. The verlet scheme already scales better, and it is
  compatible with GPUs and other accelerators.

Setting the LD random seed to 1000542586
Generated 120 of the 120 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 120 of the 120 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'N_2'
Cleaning up constraints and constant bonded interactions with virtual sites
Analysing residue names:
There are:  2493  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 12462.00

NOTE 2 [file grompp.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


Largest charge group radii for Van der Waals: 0.056, 0.056 nm
Largest charge group radii for Coulomb:   0.056, 0.056 nm
This run will generate roughly 90 Mb of data

There were 2 notes

Back Off! I just backed up topol.tpr to ./#topol.tpr.1#

gcq#454: "I never see what has been done; I only see what remains to be
done." (Marie Curie)


On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/1/17 6:07 PM, Ali Ahmed wrote:
>
>> Dear Dr. Dallas,
>> Thank you for your reply. Actually, I'm new to GROMACS and
>> I appreciate your support.
>> 
>> 
>> --
>> Here is what I get before crashing. Too many warning then crush.
>>
>>
> This is not diagnostic of anything useful.  You've been asked several
> times to provide the output of grompp, not mdrun.  The grompp output can be
> suggestive of issues you may not have considered.
>
> -Justin
>
>
> Step 37, time 0.037 (ps)  LINCS WARNING
>>
>> relative constraint deviation after LINCS:
>>
>> rms 0.002768, max 0.195102 (between atoms 34930 and 34931)
>>
>> bonds that rotated more than 30 degrees:
>>
>>   atom 1 atom 2  angle  previous, current, constraint length
>>
>>  193194   51.70.1100   0.1100  0.1100
>>
>>54409  54410   32.30.1100   0.1100  0.1100
>>
>> On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren <dallas.war...@monash.edu>
>> wrote:
>>
>> Copy the output from both of those commands, most importantly (as Mark
>>> has asked) that from the first one gmx grompp
>>>
>>> You need to show people exactly what you are seeing, not what you say
>>> you are seeing.  The latter you are filtering it, and most likely not
>>> providing all the important information.  The former allows those
>>> trying to help to see all the information that they need to see.
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Drug Delivery, Disposition and Dynamics
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3052
>>> dallas.war...@monash.edu
>>> -
>>> When the only tool you own is a hammer, every problem begins to resemble
>>> a
>>> nail.
>>>
>>>
>>> On 2 August 2017 at 04:05, Ali Ahmed <aa5635...@gmail.com> wrote:
>>>
>>>> Hi,
>>>> Thank you for your help.
>>>>
>>>> well I used this command
>>>>
>>>> gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
>>>> gmx mdrun -v -deffnm em
>>>>
>>>> and I got all the warnings. Here is my em.mdp
>>>> 
>>>>
>>> -
>>>
>>>>
>>>> integrator = steep
>>>>
>>>> emtol   = 10.0
>>>>
>>>> emstep  = 0.001
>>>>
>>>> nsteps  = 5
>>>>
>>>> energygrps   = system
>>>>
>>>> ; Parameters describing how to find the neighbors of each atom an

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
--
Here is what I get before crashing. Too many warning then crush.

Step 37, time 0.037 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

193194   51.70.1100   0.1100  0.1100

  54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren <dallas.war...@monash.edu>
wrote:

> Copy the output from both of those commands, most importantly (as Mark
> has asked) that from the first one gmx grompp
>
> You need to show people exactly what you are seeing, not what you say
> you are seeing.  The latter you are filtering it, and most likely not
> providing all the important information.  The former allows those
> trying to help to see all the information that they need to see.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 2 August 2017 at 04:05, Ali Ahmed <aa5635...@gmail.com> wrote:
> > Hi,
> > Thank you for your help.
> >
> > well I used this command
> >
> > gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
> > gmx mdrun -v -deffnm em
> >
> > and I got all the warnings. Here is my em.mdp
> > 
> -
> >
> > integrator = steep
> >
> > emtol   = 10.0
> >
> > emstep  = 0.001
> >
> > nsteps  = 5
> >
> > energygrps   = system
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> >
> > nstlist   = 1
> >
> > cutoff-scheme   = group
> >
> > ns_type= grid
> >
> > coulombtype= PME
> >
> > rcoulomb = 1.0
> >
> > rvdw= 1.0
> >
> > pbc  = xyz
> >
> > On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> No, only mdrun issues LINCS warnings. grompp issues different warnings,
> and
> >> I would like you to check whether you had any from grompp that you may
> not
> >> have considered. :-)
> >>
> >> Mark
> >>
> >> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed <aa5635...@gmail.com> wrote:
> >>
> >> > Dear Mark
> >> > Yes, all the warnings are from grompp.
> >> > I have no idea where is the problem in the structure or the topology
> >> > Thank you
> >> >
> >> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > Did you get any warnings from grompp?
> >> > >
> >> > > Mark
> >> > >
> >> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635...@gmail.com>
> wrote:
> >> > >
> >> > > > Hello GROMACS users,
> >> > > >
> >> > > > I'm doing MD for nitrogen, and for better electrostatic
> interactions
> >> I
> >> > > need
> >> > > > to use massless and charged virtual site. I did that but when I
> try
> >> to
> >> > do
> >> > > > energy minimization gives me LINCS warning and crush. I don't know
> >> > where
> >> > > is
> >> > > > the error I tried a lot but could not find a solution.
> >> > > > Anyone has an idea where is my error
> >> > > >
> >> > > > Here is the topology file (hand written)
> >> > > >
> >> > > > --
> >> > > >
> >> > > > [ defaults ]
> >> > > >
> >> > > > 1 3 yes 0.5 0.5
> >> > 

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp
-

integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> No, only mdrun issues LINCS warnings. grompp issues different warnings, and
> I would like you to check whether you had any from grompp that you may not
> have considered. :-)
>
> Mark
>
> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed <aa5635...@gmail.com> wrote:
>
> > Dear Mark
> > Yes, all the warnings are from grompp.
> > I have no idea where is the problem in the structure or the topology
> > Thank you
> >
> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Did you get any warnings from grompp?
> > >
> > > Mark
> > >
> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635...@gmail.com> wrote:
> > >
> > > > Hello GROMACS users,
> > > >
> > > > I'm doing MD for nitrogen, and for better electrostatic interactions
> I
> > > need
> > > > to use massless and charged virtual site. I did that but when I try
> to
> > do
> > > > energy minimization gives me LINCS warning and crush. I don't know
> > where
> > > is
> > > > the error I tried a lot but could not find a solution.
> > > > Anyone has an idea where is my error
> > > >
> > > > Here is the topology file (hand written)
> > > >
> > > > --
> > > >
> > > > [ defaults ]
> > > >
> > > > 1 3 yes 0.5 0.5
> > > >
> > > > 
> > > ;
> > > >
> > > > [ atomtypes ]
> > > >
> > > > ; name  bond_typemasscharge   ptype  sigma
> epsilon
> > > >
> > > >   OP   OP0.000   0.000A  0.330
> 0.3062
> > ;
> > > > nitrogen
> > > >
> > > >   M  M  0.000   0.000V  0.000
> > 0.000
> > > ;
> > > > virtual site
> > > >
> > > >
> > > > 
> > > 
> > > >
> > > > [ moleculetype ]
> > > >
> > > > ; name  nrexcl
> > > >
> > > > N2 2
> > > >
> > > >
> > > >
> > > > [ atoms ]
> > > >
> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> > > >
> > > >  1 OP  1N2 N1  1-0.482  14.0067
> > > >
> > > >  2 M 1N2 M1  1 0.964 0.000
> > > >
> > > >  3 OP   1N2 N2  1-0.482 14.0067
> > > >
> > > >
> > > >
> > > > [ constraints ]
> > > >
> > > > ; the N-N is fixed
> > > >
> > > > 1   3   1   0.11
> > > >
> > > >
> > > >
> > > > [ virtual_sites2 ]
> > > >
> > > > ; site  ai  aj  funct   a
> > > >
> > > >  2   1   3  1   0.5000  ; right in the mid
> > > >
> > > >
> > > >
> > > > 
> > > >
> > > > [ system ]
> > > >
> > > > N2 in vacuo
> > > >
> > > >
> > > >
> > > > [ molecules ]
> > > >
> > > > N2 1500
> > > >
> > > > 
> > > > --
> > > >
> > > > Here is the structure (N2.pdb)
> > >

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Did you get any warnings from grompp?
>
> Mark
>
> On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635...@gmail.com> wrote:
>
> > Hello GROMACS users,
> >
> > I'm doing MD for nitrogen, and for better electrostatic interactions I
> need
> > to use massless and charged virtual site. I did that but when I try to do
> > energy minimization gives me LINCS warning and crush. I don't know where
> is
> > the error I tried a lot but could not find a solution.
> > Anyone has an idea where is my error
> >
> > Here is the topology file (hand written)
> >
> > --
> >
> > [ defaults ]
> >
> > 1 3 yes 0.5 0.5
> >
> > 
> ;
> >
> > [ atomtypes ]
> >
> > ; name  bond_typemasscharge   ptype  sigma  epsilon
> >
> >   OP   OP0.000   0.000A  0.330  0.3062 ;
> > nitrogen
> >
> >   M  M  0.000   0.000V  0.000  0.000
> ;
> > virtual site
> >
> >
> > 
> 
> >
> > [ moleculetype ]
> >
> > ; name  nrexcl
> >
> > N2 2
> >
> >
> >
> > [ atoms ]
> >
> > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >
> >  1 OP  1N2 N1  1-0.482  14.0067
> >
> >  2 M 1N2 M1  1 0.964 0.000
> >
> >  3 OP   1N2 N2  1-0.482 14.0067
> >
> >
> >
> > [ constraints ]
> >
> > ; the N-N is fixed
> >
> > 1   3   1   0.11
> >
> >
> >
> > [ virtual_sites2 ]
> >
> > ; site  ai  aj  funct   a
> >
> >  2   1   3  1   0.5000  ; right in the mid
> >
> >
> >
> > 
> >
> > [ system ]
> >
> > N2 in vacuo
> >
> >
> >
> > [ molecules ]
> >
> > N2 1500
> >
> > 
> > --
> >
> > Here is the structure (N2.pdb)
> >
> > ---
> >
> > TITLE N2 with dummy masses
> >
> > REMARKTHIS IS A SIMULATION BOX
> >
> > MODEL1
> >
> > COMPNDUNNAMED
> >
> > AUTHORGENERATED BY OPEN BABEL 2.3.2
> >
> > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
> >
> > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> > 0.00   N
> >
> > ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> > 0.00  Xx
> >
> > ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> > 0.00   N
> >
> > CONECT13
> >
> > CONECT31
> >
> > MASTER000000003030
> >
> > END0
> >
> > 
> > -
> > Thank you
> > --
> > 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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[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Hello GROMACS users,

I'm doing MD for nitrogen, and for better electrostatic interactions I need
to use massless and charged virtual site. I did that but when I try to do
energy minimization gives me LINCS warning and crush. I don't know where is
the error I tried a lot but could not find a solution.
Anyone has an idea where is my error

Here is the topology file (hand written)

--

[ defaults ]

1 3 yes 0.5 0.5

;

[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma  epsilon

  OP   OP0.000   0.000A  0.330  0.3062 ;
nitrogen

  M  M  0.000   0.000V  0.000  0.000 ;
virtual site



[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

 1 OP  1N2 N1  1-0.482  14.0067

 2 M 1N2 M1  1 0.964 0.000

 3 OP   1N2 N2  1-0.482 14.0067



[ constraints ]

; the N-N is fixed

1   3   1   0.11



[ virtual_sites2 ]

; site  ai  aj  funct   a

 2   1   3  1   0.5000  ; right in the mid





[ system ]

N2 in vacuo



[ molecules ]

N2 1500


--

Here is the structure (N2.pdb)

---

TITLE N2 with dummy masses

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1

ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
0.00   N

ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
0.00  Xx

ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
0.00   N

CONECT13

CONECT31

MASTER000000003030

END0


-
Thank you
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Re: [gmx-users] nitrogen itp file with virtual site

[Ali Ahmed]

Dear Justin
I have checked and tried but still not working, it says ( invalid order for
directive atomtypes). Please can you take a look on the following

Here is the topology file

;virtual sites have zero mass which leads to zero Moment of inertia

;virual sites have charge only 0.482 e. to balance the nitrogen atom
negative charge -0.482 e.

;the distance between two nitrogn atoms is 0.11 nm

;the distance between two virtual sites is 0.15 nm

;the distance between nitrogen atom and virtual site is 0.02 nm. This makes
the virtual site attached to the nitrogen atom

[ atomtypes ]

;name bond_type mass   charge  ptypesigma   epsilon

N N 0.000  0.000  A 0.332
0.3026

MM0.000  0.000  V  0.000
0.000 ;

[ moleculetype ]

; name  nrexcl

N_2   2

[ atoms ]

;   nr   typeresnr residue atom   cgnrcharge   mass
typeBchargeB  massB

 1 N   1N_2 N1  1-0.48214.0067

 2 N   1N_2 N2  1-0.48214.0067

 3 M   1N_2 M1  1 0.4820.  ; MN
is the virtual site

 4 M   1N_2 M2  1 0.4820.



[ constraints ]

; There are no bonds in this system

; Instead, we fix the distance between the mass centers such that

; the virtual sites can be reconstructed

1   2   1   0.11



[ system ]

Nitrogen  in vacuo



[ molecules ]

N_2 1000

-

here is the pdb file



TITLE N_2 with dummy masses

REMARKTHIS IS A SIMULATION BOX

CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1

MODEL1

ATOM  1  N1  N_2 1   0.000   0.000   0.000  1.00  0.00


ATOM  2  N2  N_2 1   1.100   0.000   0.000  1.00  0.00


ATOM  3  M1  N_2 1   0.200   0.000   0.000  1.00  0.00


ATOM  4  M2  N_2 1   0.900   0.000   0.000  1.00  0.00



TER

ENDMDL

---

Thank you

On Tue, Jul 18, 2017 at 8:10 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/17/17 3:39 PM, Ali Ahmed wrote:
>
>> Dear Justin
>>
>> Here is the topology file I wrote. I included all the parameters rather
>> than use a specific FF.
>>
>> Thank you for your support
>>
>> ..
>>
>> 
>> -
>>
>> ; virtual sites have zero mass which leads to zero Moment of inertia
>>
>> ;virual sites have charge only 0.482 e. to balance the nitrogen atom
>> negative charge -0.482 e.
>>
>> ; the distance between two nitrogn atoms N--N is 0.11 nm
>>
>> ;the distance between two virtual sites is 0.15 nm
>>
>> ;the distance between nitrogen atom and virtual site is 0.02 nm. This
>> makes
>> the virtual site attached to the nitrogen atom
>>
>> ;
>>
>> [ atomtypes ]
>>
>> ; name  bond_typemasscharge   ptype  sigma  epsilon
>>
>> N   N 0.000   0.000  A
>> 0.332  0.3026
>>
>>MN   MN 0.000   0.000  A  0.000
>> 0.000; MN is the virtual sites
>>
>>
> This is incorrect; the virtual site should be particle type V, not A.
>
>
>>
>> [ moleculetype ]
>>
>> ; name  nrexcl
>>
>> N_2   2
>>
>>
>>
>> [ atoms ]
>>
>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>> typeBchargeB  massB
>>
>>   1 N   1N_2 N1  1-0.482
>> 14.0067
>>
>>   2 N   1N_2 N2  1-0.482
>> 14.0067
>>
>>   3MN   1N_2 M11 0.482
>> 0.
>>
>>   4MN   1N_2 M2 1 0.482
>> 0.
>>
>>
>>
>> [ constraints ]
>>
>> ; There are no bonds in this system
>>
>> ; Instead, we fix the distance between the mass centers such that
>>
>> ; the virtual sites can be reconstructed
>>
>>  3   4   1   0.15
>>
>>
> This is why your system is failing.  You're defining a constraint between
> the virtual sites and no bonded interaction at all between the N atoms.  If
> the N-N bond is to be constant at 0.11 nm, then set it as a constraint
> (between atoms 1 and 2) and construct the virtual sites based on the real
> atoms in the system.
>
> -Justin

Re: [gmx-users] nitrogen itp file with virtual site

[Ali Ahmed]

Dear Justin

Here is the topology file I wrote. I included all the parameters rather
than use a specific FF.

Thank you for your support

..

-

; virtual sites have zero mass which leads to zero Moment of inertia

;virual sites have charge only 0.482 e. to balance the nitrogen atom
negative charge -0.482 e.

; the distance between two nitrogn atoms N--N is 0.11 nm

;the distance between two virtual sites is 0.15 nm

;the distance between nitrogen atom and virtual site is 0.02 nm. This makes
the virtual site attached to the nitrogen atom

;

[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma  epsilon

   N   N 0.000   0.000  A
0.332  0.3026

  MN   MN 0.000   0.000  A  0.000
0.000; MN is the virtual sites



[ moleculetype ]

; name  nrexcl

N_2   2



[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB

 1 N   1N_2 N1  1-0.482
14.0067

 2 N   1N_2 N2  1-0.482
14.0067

 3MN   1N_2 M11 0.482
0.

 4MN   1N_2 M2 1 0.4820.



[ constraints ]

; There are no bonds in this system

; Instead, we fix the distance between the mass centers such that

; the virtual sites can be reconstructed

3   4   1   0.15

[ system ]

CO2 in vacuo



[ molecules ]

N_2 30



On Mon, Jul 17, 2017 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/17/17 12:31 PM, Ali Ahmed wrote:
>
>> Dear Justin
>> I have tried same what you have said. I followed the tutorial for CO2 but
>> didn't work, gave an error during the energy minimization . I'm not sure
>> what was the wrong, I noticed the N atoms (in the box) were separated from
>> the virtual site after the error.
>>
>>
> If you have just N2 in a box in vacuo, then this would suggest a topology
> problem.  Please post the exact text of your .itp file.  It should be quite
> short and easy to spot any problems.
>
> -Justin
>
>
>
>> On Mon, Jul 17, 2017 at 10:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 7/17/17 11:38 AM, Ali Ahmed wrote:
>>>
>>> Dear Justin
>>>> Thank you very much. As I saw in some literature (as in the link below)
>>>> that N atom has a negative charge and needs a massless positive charge.
>>>> I
>>>> tried with most of the FFs but could not produce nitrogen density above
>>>> critical point. I don'n know which FF is the best one and I'm new to MD
>>>> simulations and new GROMACS user.
>>>> Could you please tell me which FF should I use?
>>>>
>>>>
>>> What you're citing is a custom model.  You can write the force field
>>> files
>>> very easily.  I see what you're trying to do now, but you should be clear
>>> that N2 is not a negatively charged molecule simply because the N atoms
>>> (in
>>> this representation) have partial negative charges.  The virtual site
>>> balances it out so that electrostatic properties are better represented.
>>>
>>> The virtual site you need to create is a simple one, placed at the center
>>> of the N-N bond, so this is virtual_sites2 with an "a" value of 0.5.
>>>
>>> -Justin
>>>
>>>
>>> Thank you very much I appreciate your support.
>>>
>>>>
>>>> http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta
>>>>
>>>> On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 7/16/17 9:20 PM, Ali Ahmed wrote:
>>>>>
>>>>> Hello GROMACS users,
>>>>>
>>>>>> This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
>>>>>> super critical point.The structure I use is different from regular
>>>>>> nitrogen
>>>>>> (N-N). As you know N atom has a negative charge which means the
>>>>>> nitrogen
>>>>>> molecule will be negatively charged, therefore I need to use massless
>>>>>> and
>>>>>>
>>>>>>
>>>>>> This is incorrect - N2 carries no formal charge.
>>>>>
>>>>> charged virtual site to equilibrate the molecule. I have looked on the
>>>>>
>&g

Re: [gmx-users] nitrogen itp file with virtual site

[Ali Ahmed]

Dear Justin
I have tried same what you have said. I followed the tutorial for CO2 but
didn't work, gave an error during the energy minimization . I'm not sure
what was the wrong, I noticed the N atoms (in the box) were separated from
the virtual site after the error.


On Mon, Jul 17, 2017 at 10:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/17/17 11:38 AM, Ali Ahmed wrote:
>
>> Dear Justin
>> Thank you very much. As I saw in some literature (as in the link below)
>> that N atom has a negative charge and needs a massless positive charge. I
>> tried with most of the FFs but could not produce nitrogen density above
>> critical point. I don'n know which FF is the best one and I'm new to MD
>> simulations and new GROMACS user.
>> Could you please tell me which FF should I use?
>>
>
> What you're citing is a custom model.  You can write the force field files
> very easily.  I see what you're trying to do now, but you should be clear
> that N2 is not a negatively charged molecule simply because the N atoms (in
> this representation) have partial negative charges.  The virtual site
> balances it out so that electrostatic properties are better represented.
>
> The virtual site you need to create is a simple one, placed at the center
> of the N-N bond, so this is virtual_sites2 with an "a" value of 0.5.
>
> -Justin
>
>
> Thank you very much I appreciate your support.
>>
>> http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta
>>
>> On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 7/16/17 9:20 PM, Ali Ahmed wrote:
>>>
>>> Hello GROMACS users,
>>>> This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
>>>> super critical point.The structure I use is different from regular
>>>> nitrogen
>>>> (N-N). As you know N atom has a negative charge which means the nitrogen
>>>> molecule will be negatively charged, therefore I need to use massless
>>>> and
>>>>
>>>>
>>> This is incorrect - N2 carries no formal charge.
>>>
>>> charged virtual site to equilibrate the molecule. I have looked on the
>>>
>>>> tutorial about CO2 to produce the XXX.itp but didnot work with me. Could
>>>> anyone have done it before tell me how to do it ?
>>>>
>>>>
>>>> You don't need virtual sites for a diatomic molecule.
>>>
>>> -Justin
>>>
>>> Here are the parameters:
>>>
>>>> N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge
>>>> =(-0.482 e).
>>>>
>>>> XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge=
>>>> 0.964
>>>> e.
>>>>
>>>> Thank you very much.
>>>>
>>>>
>>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at 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.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] nitrogen itp file with virtual site

[Ali Ahmed]

Dear Justin
Thank you very much. As I saw in some literature (as in the link below)
that N atom has a negative charge and needs a massless positive charge. I
tried with most of the FFs but could not produce nitrogen density above
critical point. I don'n know which FF is the best one and I'm new to MD
simulations and new GROMACS user.
Could you please tell me which FF should I use?
Thank you very much I appreciate your support.

http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta

On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/16/17 9:20 PM, Ali Ahmed wrote:
>
>> Hello GROMACS users,
>> This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
>> super critical point.The structure I use is different from regular
>> nitrogen
>> (N-N). As you know N atom has a negative charge which means the nitrogen
>> molecule will be negatively charged, therefore I need to use massless and
>>
>
> This is incorrect - N2 carries no formal charge.
>
> charged virtual site to equilibrate the molecule. I have looked on the
>> tutorial about CO2 to produce the XXX.itp but didnot work with me. Could
>> anyone have done it before tell me how to do it ?
>>
>>
> You don't need virtual sites for a diatomic molecule.
>
> -Justin
>
> Here are the parameters:
>> N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge
>> =(-0.482 e).
>>
>> XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge= 0.964
>> e.
>>
>> Thank you very much.
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at 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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[gmx-users] nitrogen itp file with virtual site

[Ali Ahmed]

Hello GROMACS users,
This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
super critical point.The structure I use is different from regular nitrogen
(N-N). As you know N atom has a negative charge which means the nitrogen
molecule will be negatively charged, therefore I need to use massless and
charged virtual site to equilibrate the molecule. I have looked on the
tutorial about CO2 to produce the XXX.itp but didnot work with me. Could
anyone have done it before tell me how to do it ?

Here are the parameters:
N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge
=(-0.482 e).

XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge= 0.964
e.

Thank you very much.
-- 
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