Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

[Zoe Chan]

Dear Gerrit,


After trying a few different settings of .mdp, I found that "cutoff-scheme = 
Verlet" and "QMMMscheme = ONIOM" were causing the error.  Would you have any 
idea how were these two settings linked to the generation of ".pc" file, and 
what would you suggest if I have to run under ONIOM?


Thank you.


Best regards,

Zoe



From: CHAN, Zoe ZC [Student] 
Sent: 27 November 2017 18:23
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Dear Gerrit,

Thank you very much for your prompt reply.
I’ve tried to run the simulation with wenjin’s tutorial and it passed the point 
charge correction step with no problem. I compared the “.out” output files of 
my protein and of the tutorial peptide, I noticed there’s a line “%pointcharges 
“peptide.pc”” at the end of the input file section, I guess it shows that the 
basename has been linked to the “.pc” point charge file instead of the default 
name “temp.pc”, and it’s missing in my protein’s output file. Would that have 
possibly caused the crash?
Again, thank you for your help.

Best regards,
Zoe

On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit 
mailto:ggro...@gwdg.de>> wrote:

>From the error message it seems that ORCA program crashes. Unfortunately, Orca 
>is no longer supported, which means that if the ORCA's input or anything else 
>has changed, the gromacs interface may fail.

What you could try is to use the version of ORCA that others have used before.

Best,

Gerrit





Content-Type: text/plain; charset="iso-8859-1"

Dear Gromacs Users,


I've been running a QM/MM calculation on a protein with fluorescence probe, 
using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1.  The following 
lines were included in the .mdp file,


QMMM = yes
QMMM-grps= QMatoms
QMmethod  = B3LYP
QMbasis  = 6-31G*
QMMMscheme   = ONIOM
QMcharge   = -2
QMmult= 2

The run was aborted with the error messages,


FATAL ERROR ENCOUNTERED
CANNOT OPEN FILE
Filename: temp.pc

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee]
[ 2] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98]
[ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0]
[ 4] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647]
[ 5] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9]
[ 6] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b]
[ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef]
[ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33]
[ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172]
[10] mdrun_mpi_d(cmain+0x1a17)[0x433f67]
[11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830]
[12] mdrun_mpi_d(_start+0x29)[0x4072b9]
*** End of error message ***
Segmentation fault (core dumped)


I am clueless on where the error came from, would anyone have any insight?  
Thank you.


Best regards,

Zoe

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Re: [gmx-users] Metal-Protein interactions

[Justin Lemkul]

On 11/28/17 1:00 PM, RAHUL SURESH wrote:

On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul  wrote:



On 11/28/17 4:54 AM, RAHUL SURESH wrote:

I am trying to simulate a metal-protein interaction using gromacs 2016
package and charmm36 ff.
I have prepared the initial pdb by performing an oniom calculations

between

protein and metal (at various positions) using gaussian 09 and chose the
structure with maximum binding energy. The metal ion is bonded to oxygen
atom of His residue. Having a look at gro file after each step

That's unusual; His typically coordinate metals via their delta or
epsilon N atoms.


Sorry that I pronounced wrongly as oxygen.. regret the inconvenience.


(protein.gro, em.gro, nvt.groand npt.gro) the distance between metal  ion
and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over the
course of simulations for 10ns, the metal ion is away from the protein.

What can be done to have the metal ion restrained at its position? Or if

I

extend the simulation will the metal ion find its appropritae position
during the course time?

Unlikely. This is a fundamental issue with classical mechanical force
fields approximating ion interactions very poorly, particularly in the
case of multivalent and/or transition metals. There are many effects
like polarization and charge transfer that simply can't be modeled. You
can apply distance restraints (or actual covalent bonds), NBFIX LJ
parameters, etc.

while restraing the metal ion, it arise an error stating that an atom can
not be mentioned in two groups.
Tc grps = protein_cu water_and_ions.
Cu will already be mentioned in ions.


It should be grouped with the protein; a coordinated metal is 
functionally part of the protein and should be treated as such. It makes 
no sense to couple it to the solvent thermostat.



and that may be enough to preserve the binding pose. In

reality, one would have to reparametrize any ligating residues because
the charge distribution on the ion and anything coordinating it is not
at all what the standard force field uses.

Reparameterize.? Means I have to add additional parameter file to the
charmm36 ff after interacting with metal ion.?


It means you would have to derive new residue definitions, but a QM/MM 
approach is probably superior.




Also Justin, what if I can manually add a bond between N of HIS and metal
ion with most appropriate bond length ..?
(To avoid complexity if it works)


Yes, that is a possibility, but again you will have to do some QM work 
to properly parametrize the geometries and vibrational frequencies for 
the new bonded parameters (which then include angles and dihedrals). 
Cu2+ is a difficult ion to deal with, though, so this may be 
surprisingly laborious.


-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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Re: [gmx-users] GROMACS 2018 first beta released

[Åke Sandgren]

First tests hints at ~10% better performance on Broadwell CPUs compared
to 2016.4 on the ion_channel case we got from Erik L.

This using the same compiler toolchain version.

Will test more tomorrow :-)

On 11/28/2017 07:09 PM, Mark Abraham wrote:
> 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!


-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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Re: [gmx-users] Pressure through one direction

[Wes Barnett]

On Tue, Nov 28, 2017 at 12:25 PM, ali akgün  wrote:

> Hi,
>
> Can i generate mdp file for pressure through one direction system.For
> example:
>
> Ref pressure:
>
> X direction:1.0 bar
> Other direction:  0.0 bar
>


Yes, see the options here:
http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html


-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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[gmx-users] GROMACS 2018 first beta released

[Mark Abraham]

Hi GROMACS users,

The first 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!

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-beta1.tar.gz
Documentation: http://manual.gromacs.org/documentation/2018-beta1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2018-beta1/ReleaseNotes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2018-beta1.tar.gz

Happy testing!

Mark Abraham
GROMACS Development Manager
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Re: [gmx-users] Metal-Protein interactions

[RAHUL SURESH]

On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul  wrote:

>
>
> On 11/28/17 4:54 AM, RAHUL SURESH wrote:
> > I am trying to simulate a metal-protein interaction using gromacs 2016
> > package and charmm36 ff.
> > I have prepared the initial pdb by performing an oniom calculations
> between
> > protein and metal (at various positions) using gaussian 09 and chose the
> > structure with maximum binding energy. The metal ion is bonded to oxygen
> > atom of His residue. Having a look at gro file after each step
> That's unusual; His typically coordinate metals via their delta or
> epsilon N atoms.
>
Sorry that I pronounced wrongly as oxygen.. regret the inconvenience.

>
> > (protein.gro, em.gro, nvt.groand npt.gro) the distance between metal  ion
> > and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over the
> > course of simulations for 10ns, the metal ion is away from the protein.
> >
> > What can be done to have the metal ion restrained at its position? Or if
> I
> > extend the simulation will the metal ion find its appropritae position
> > during the course time?
>
> Unlikely. This is a fundamental issue with classical mechanical force
> fields approximating ion interactions very poorly, particularly in the
> case of multivalent and/or transition metals. There are many effects
> like polarization and charge transfer that simply can't be modeled. You
> can apply distance restraints (or actual covalent bonds), NBFIX LJ
> parameters, etc.

while restraing the metal ion, it arise an error stating that an atom can
not be mentioned in two groups.
Tc grps = protein_cu water_and_ions.
Cu will already be mentioned in ions.

and that may be enough to preserve the binding pose. In
> reality, one would have to reparametrize any ligating residues because
> the charge distribution on the ion and anything coordinating it is not
> at all what the standard force field uses.

Reparameterize.? Means I have to add additional parameter file to the
charmm36 ff after interacting with metal ion.?


Also Justin, what if I can manually add a bond between N of HIS and metal
ion with most appropriate bond length ..?
(To avoid complexity if it works)

Thank you

>
>
> -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
>
> ==
>
> --
> Gromacs Users mailing list
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> posting!
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Not enough memory. Failed to realloc

[RAHUL SURESH]

Hi

Yeah. I understood that.. thanks a lot for your patience

On Tue, 28 Nov 2017 at 7:10 PM, Justin Lemkul  wrote:

>
>
> On 11/27/17 11:55 PM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > It worked. Actually by its own. I reconstructed the pdb and gave again.
>
> For the sake of completeness, the original problem was indeed due to a
> massive box size, which was probably just incorrectly set. You had a
> 92-nm y-box vector and as a result, solvate was trying to add nearly 28
> million(!) water molecules. This would definitely exhaust memory on
> nearly any common computer.
>
> -Justin
>
> > Thank you so much for your time
> >
> > On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH 
> > wrote:
> >
> >> This error occur only for this particular pdb structure. The protein
> here
> >> is attached with a metal ion. The necessary changes are made to the
> >> charmm36 ff.
> >>
> >> Should be some error in my pdb?
> >>
> >> On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH  >
> >> wrote:
> >>
> >>> Here i have added the report for the commands
> >>>
> >>>
> >>> Command line:
> >>>*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
> >>>
> >>> Read 628 atoms
> >>> Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
> >>> No velocities found
> >>>  system size :  3.716 91.693  1.702 (nm)
> >>>  diameter: 91.698   (nm)
> >>>  center  : -0.048  0.153  0.001 (nm)
> >>>  box vectors :  3.715 91.693  1.702 (nm)
> >>>  box angles  :  90.00  90.00  90.00 (degrees)
> >>>  box volume  : 579.93   (nm^3)
> >>>  shift   : 46.897 46.696 46.848 (nm)
> >>> new center  : 46.849 46.849 46.849 (nm)
> >>> new box vectors : 93.698 93.698 93.698 (nm)
> >>> new box angles  :  90.00  90.00  90.00 (degrees)
> >>> new box volume  :822615.31   (nm^3)
> >>>
> >>>
> >>> Command line:
> >>>*gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*
> >>>
> >>> Reading solute configuration
> >>> GROup of MAchos and Cynical Suckers
> >>> Containing 628 atoms in 43 residues
> >>> Reading solvent configuration
> >>> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
> >>> Containing 648 atoms in 216 residues
> >>>
> >>> Initialising inter-atomic distances...
> >>>
> >>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
> >>>   based on residue and atom names, since they could not be
> >>>   definitively assigned from the information in your input
> >>>   files. These guessed numbers might deviate from the mass
> >>>   and radius of the atom type. Please check the output
> >>>   files if necessary.
> >>>
> >>> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
> >>> from the source below. This means the results may be different
> >>> compared to previous GROMACS versions.
> >>>
> >>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
> >>> A. Bondi
> >>> van der Waals Volumes and Radii
> >>> J. Phys. Chem. 68 (1964) pp. 441-451
> >>>   --- Thank You ---  
> >>>
> >>> Generating solvent configuration
> >>> Will generate new solvent configuration of 51x51x51 boxes
> >>> Solvent box contains 83316213 atoms in 27772071 residues
> >>>
> >>> ---
> >>> Program: gmx solvate, version 2016.4
> >>>
> >>> Memory allocation failed:
> >>> std::bad_alloc
> >>>
> >>> For more information and tips for troubleshooting, please check the
> >>> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>>
> >>>
> >>> On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul 
> wrote:
> >>>
> 
>  On 11/27/17 11:26 AM, RAHUL SURESH wrote:
> 
> > Hi
> >
> >
> >
> > *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
> >
>  And how large is the resulting box? Are all the coordinates properly
>  defined? What is the full screen output of gmx solvate up to the
> failure?
> 
>  -Justin
> 
> 
>  I have used the above command to generate the box. Infact I have used
> > this
> > command before and I never got any error.
> >
> > Thank you
> >
> > On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul 
> wrote:
> >
> >
> >> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
> >>
> >> Dear Users
> >>> I am trying to carryout protein-metal interaction using charmm36
> ff.
> >>> During
> >>> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
> >>> solv.gro"
> >>> *i receive a error stating
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes
> >>> for
> >>> atoms_->atom,atoms_->atom=0(called from
> >>> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
> >>> topology/atomsbuilder.cpp,line
> >>> 86)". *
> >>> I have enough space to carry out t

[gmx-users] Pressure through one direction

[ali akgün]

Hi,

Can i generate mdp file for pressure through one direction system.For
example:

Ref pressure:

X direction:1.0 bar
Other direction:  0.0 bar

Thank you.
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Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

[GIANMARCO BARTALINI]

Thanks, but it doesn't work. Same problem.

Gianmarco Bartalini

Il 27 nov 2017 14:37, "Justin Lemkul"  ha scritto:

>
>
> On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:
>
>> Hello guys, I produced a system "protein + lipid membrane" using the
>> online
>> tool CHARMM-GUI. Since I need to use the Amber force field, I added the
>> Lipids17 force field inside Gromacs. The implementation should work fine,
>> since the conversion of an equilibrated structure produces a nice and
>> correct gro file. But when I try to convert the (not minimized) PDB file
>> that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
>> lipid molecules are melted together (due to their bad distances). If I use
>> this structure for a minimization, the calculation stops due to bad
>> energies. Do you know how to solve this issue?
>>
>
> This isn't a pdb2gmx problem so much as it is a quirk of how CHARMM-GUI
> creates lipid membranes. There is almost always overlap between tail atoms
> in the different lipid leaflets. The CHARMM minimizer deals with these just
> fine, but GROMACS almost always chokes. The reason is that GROMACS sets a
> rather aggressive default EM step size of 0.02 nm, whereas the CHARMM
> minimizer defaults to 0.002. Lower the value of emstep and see if it
> proceeds correctly. That has always worked for us.
>
> -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
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani  wrote:

>
>
> On Mon, Nov 27, 2017 at 1:55 AM, Alex  wrote:
>
>> Hi,
>>
>> The answer is clearly in the error, just read it please:
>> 2.848793 > 0.49 * (4/2) where 4 is the box length.
>>
>>> But i choose ( by pull_coord1_dim) Z direction for pulling (12 nm not
>>> 4nm), it doesn't mean that protein should just get closer to ZnS(sheet) in
>>> Z direction?
>>
>>  thank you so much
>>
>>
>>
>> You can either keep the “pull_coord1_geometry= distance” and increase
>> the box length or change the “pull_coord1_geometry” to  “=
>> direction-periodic“. I prefer the former though.
>>
>> Cheers,
>> Alex
>>
>>> I've got it.
>>
>> would you please answer to another questions too? thank you in advance
>>
>>
>
>>
>>
>> On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:
>>
>> > Hi;
>> >
>> > This is md_pull.mdp
>> >
>> > integrator   = md
>> > dt   = 0.001
>> > nsteps   = 200
>> > nstxout  = 0
>> > nstvout  = 0
>> > nstfout  = 0
>> > nstlog   = 500
>> > nstenergy= 1000
>> > nstxtcout= 1000
>> > rlist= 1.5
>> > rcoulomb = 1.5
>> > rvdw = 1.2
>> > coulombtype  = pme
>> > cutoff-scheme= group
>> > vdwtype  = Switch
>> > rvdw_switch  = 1.0
>> > pcoupl   = no
>> > gen-vel  = yes
>> > gen-temp = 0
>> > gen-seed = 173529
>> > constraints  = h-bonds
>> > pbc  = xy
>> > freezegrps   = WAL ZnS
>> > freezedim= Y Y Y Y Y Y
>> > energygrp-excl   = WAL WAL ZnS ZnS
>> > energygrps   = SOL WAL ZnS Protein NA CL
>> > nwall= 2
>> > wall-atomtype= C C
>> > wall-type= 9-3
>> > wall-density = 150 150
>> > wall-ewald-zfac  = 3
>> > ewald-geometry   = 3dc
>> > fourierspacing   = 0.12
>> > tcoupl   = v-rescale
>> > tc-grps  = System
>> > tau-t= 0.1
>> > ref-t= 300
>> > pull= yes
>> > pull_ngroups= 2
>> > pull_ncoords= 1
>> > pull_group1_name= ZnS
>> > pull_group2_name= Protein
>> > pull_coord1_type= umbrella
>> > pull_coord1_geometry= distance
>> > pull_coord1_groups  = 1 2
>> > pull__coord1_dim= N N Y
>> > pull_coord1_rate  = -0.001; 1 nm per  ns
>> > pull_coord1_k = 5000
>> > pull_coord1_start  = yes
>> >
>> > Program gmx grompp, VERSION 5.1.4
>> >
>> > Fatal error:
>> > Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
>> > times the box size (2.00).
>> > You might want to consider using "pull-geometry = direction-periodic"
>> > instead.
>> >
>> > the box size is= 4 4 12
>> >
>> > could you please help me to resolve it?
>> > -
>> > Mr.Lemkul told me rcutt-off is wrong and
>> >
>> >  i should'nt put "cutoff-scheme= group" >>>but when i remove
>> > it i'll get  this error too;
>> >
>> >   >>With Verlet lists rcoulomb!=rvdw is not supported
>> >
>> > i know it's wrong solution but what is my alternative?!!
>> >
>> > --
>> > -dummy particle should move towards the surface with a constant speed
>> of 1
>> > nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
>> > corresponding to the spring constant of 5000.
>> >
>> > I DON'T know how should i implement deltaZ(=2)? which .mdp option
>> refers to
>> > it?!
>> >
>> > thank you so much
>> >
>> > Best regards
>> > Rose
>> > --
>> > 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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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/28/17 10:00 AM, rose rahmani wrote:

Would "pull_geometry=periodic-distance" be another solution for it?


No. That affects how the reaction coordinate distance is calculated, not 
the PBC treatment, which is intrinsic to any simulation using PBC.


-Justin


On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:



On 11/28/17 12:23 AM, rose rahmani wrote:


Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?


Bonds can't break and molecules can't "disintegrate" - what you're seeing
is probably a result of PBC.

http://www.gromacs.org/Documentation/Terminology/Periodic_
Boundary_Conditions


-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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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Umbrella sampling

[rose rahmani]

Would "pull_geometry=periodic-distance" be another solution for it?

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul  wrote:

>
>
> On 11/28/17 12:23 AM, rose rahmani wrote:
>
>> Hello;
>>
>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>> till almost conf1000.gro(and a little more). But in for example
>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>> please help me?
>>
>
> Bonds can't break and molecules can't "disintegrate" - what you're seeing
> is probably a result of PBC.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
> Boundary_Conditions
>
>
> -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
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] Metal-Protein interactions

[Justin Lemkul]

On 11/28/17 4:54 AM, RAHUL SURESH wrote:

I am trying to simulate a metal-protein interaction using gromacs 2016
package and charmm36 ff.
I have prepared the initial pdb by performing an oniom calculations between
protein and metal (at various positions) using gaussian 09 and chose the
structure with maximum binding energy. The metal ion is bonded to oxygen
atom of His residue. Having a look at gro file after each step
That's unusual; His typically coordinate metals via their delta or 
epsilon N atoms.



(protein.gro, em.gro, nvt.groand npt.gro) the distance between metal  ion
and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over the
course of simulations for 10ns, the metal ion is away from the protein.

What can be done to have the metal ion restrained at its position? Or if I
extend the simulation will the metal ion find its appropritae position
during the course time?


Unlikely. This is a fundamental issue with classical mechanical force 
fields approximating ion interactions very poorly, particularly in the 
case of multivalent and/or transition metals. There are many effects 
like polarization and charge transfer that simply can't be modeled. You 
can apply distance restraints (or actual covalent bonds), NBFIX LJ 
parameters, etc. and that may be enough to preserve the binding pose. In 
reality, one would have to reparametrize any ligating residues because 
the charge distribution on the ion and anything coordinating it is not 
at all what the standard force field uses.


-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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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/28/17 12:23 AM, rose rahmani wrote:

Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?


Bonds can't break and molecules can't "disintegrate" - what you're 
seeing is probably a result of PBC.


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-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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Re: [gmx-users] Not enough memory. Failed to realloc

[Justin Lemkul]

On 11/27/17 11:55 PM, RAHUL SURESH wrote:

Dear Justin

It worked. Actually by its own. I reconstructed the pdb and gave again.


For the sake of completeness, the original problem was indeed due to a 
massive box size, which was probably just incorrectly set. You had a 
92-nm y-box vector and as a result, solvate was trying to add nearly 28 
million(!) water molecules. This would definitely exhaust memory on 
nearly any common computer.


-Justin


Thank you so much for your time

On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH 
wrote:


This error occur only for this particular pdb structure. The protein here
is attached with a metal ion. The necessary changes are made to the
charmm36 ff.

Should be some error in my pdb?

On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH 
wrote:


Here i have added the report for the commands


Command line:
   *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*

Read 628 atoms
Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
No velocities found
 system size :  3.716 91.693  1.702 (nm)
 diameter: 91.698   (nm)
 center  : -0.048  0.153  0.001 (nm)
 box vectors :  3.715 91.693  1.702 (nm)
 box angles  :  90.00  90.00  90.00 (degrees)
 box volume  : 579.93   (nm^3)
 shift   : 46.897 46.696 46.848 (nm)
new center  : 46.849 46.849 46.849 (nm)
new box vectors : 93.698 93.698 93.698 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :822615.31   (nm^3)


Command line:
   *gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*

Reading solute configuration
GROup of MAchos and Cynical Suckers
Containing 628 atoms in 43 residues
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues

Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
  based on residue and atom names, since they could not be
  definitively assigned from the information in your input
  files. These guessed numbers might deviate from the mass
  and radius of the atom type. Please check the output
  files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
  --- Thank You ---  

Generating solvent configuration
Will generate new solvent configuration of 51x51x51 boxes
Solvent box contains 83316213 atoms in 27772071 residues

---
Program: gmx solvate, version 2016.4

Memory allocation failed:
std::bad_alloc

For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors


On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul  wrote:



On 11/27/17 11:26 AM, RAHUL SURESH wrote:


Hi



*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*


And how large is the resulting box? Are all the coordinates properly
defined? What is the full screen output of gmx solvate up to the failure?

-Justin


I have used the above command to generate the box. Infact I have used

this
command before and I never got any error.

Thank you

On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul  wrote:



On 11/27/17 7:17 AM, RAHUL SURESH wrote:

Dear Users

I am trying to carryout protein-metal interaction using charmm36 ff.
During
solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
solv.gro"
*i receive a error stating








*"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes
for
atoms_->atom,atoms_->atom=0(called from
file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
topology/atomsbuilder.cpp,line
86)". *
I have enough space to carry out this simulation and I am using 2016
version of gromacs.

How large is your box? Are you sure you have set its size in nm, not

A?

-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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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemist

[gmx-users] Metal-Protein interactions

[RAHUL SURESH]

I am trying to simulate a metal-protein interaction using gromacs 2016
package and charmm36 ff.
I have prepared the initial pdb by performing an oniom calculations between
protein and metal (at various positions) using gaussian 09 and chose the
structure with maximum binding energy. The metal ion is bonded to oxygen
atom of His residue. Having a look at gro file after each step
(protein.gro, em.gro, nvt.groand npt.gro) the distance between metal  ion
and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over the
course of simulations for 10ns, the metal ion is away from the protein.

What can be done to have the metal ion restrained at its position? Or if I
extend the simulation will the metal ion find its appropritae position
during the course time?

Sounds dramatic I guess, but still that remains in my mind.

Thank you

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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