date:20180725

>
>>
> It's in $GMXLIB. It's not a per-force field thing.
>

Ah, in that case I think it might be more appropriate to modify my scripts
with selections, etc. Not a big deal, thanks.

>
>
>>
> This file is only used by pdb2gmx, so depending on how you're generating
> topologies, it may not matter.
>
> I don't use pdb2gmx, but good to know. Now the challenge is not to forget.
:)

Alex
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Re: [gmx-users] grouping custom ions





On 7/25/18 5:12 PM, Alex wrote:

Ah. Upon actually checking my oplsaa.ff directory, i don't have this file.
Could this info be somewhere else?


It's in $GMXLIB. It's not a per-force field thing.


Another question, while we're at it: the file 'atomtypes.atp' is basically
a table with atomic masses. Over a few years, I have added a bunch of new
atomtypes without modifying this file. Would that be a problem?


This file is only used by pdb2gmx, so depending on how you're generating 
topologies, it may not matter.


-Justin


Thanks,

Alex

On Wed, Jul 25, 2018 at 2:36 PM, Justin Lemkul  wrote:



On 7/25/18 4:35 PM, Alex wrote:


Hi all,

Perhaps a trivial question here. I added a few custom metal ions into
oplsaa's 'ions.itp' and 'ffnonbonded.itp' -- everything works fine. There
is, however, a problem with selecting them in e.g. trjconv without using a
custom index. Example: 5 NA, 6 CL, and 1 XX (custom) ions in the system.
The group "Ion" now only contains 11 elements (NA + CL), while I'd like to
select all 12 with "Ion". Things are scripted, so it would be really nice
to be able to do that without additional indexing.



Update residuetypes.dat to include your new ions.

-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.thelemkullab.com

==

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==

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.thelemkullab.com

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Re: [gmx-users] grouping custom ions

Ah. Upon actually checking my oplsaa.ff directory, i don't have this file.
Could this info be somewhere else?
Another question, while we're at it: the file 'atomtypes.atp' is basically
a table with atomic masses. Over a few years, I have added a bunch of new
atomtypes without modifying this file. Would that be a problem?

Thanks,

Alex

On Wed, Jul 25, 2018 at 2:36 PM, Justin Lemkul  wrote:

>
>
> On 7/25/18 4:35 PM, Alex wrote:
>
>> Hi all,
>>
>> Perhaps a trivial question here. I added a few custom metal ions into
>> oplsaa's 'ions.itp' and 'ffnonbonded.itp' -- everything works fine. There
>> is, however, a problem with selecting them in e.g. trjconv without using a
>> custom index. Example: 5 NA, 6 CL, and 1 XX (custom) ions in the system.
>> The group "Ion" now only contains 11 elements (NA + CL), while I'd like to
>> select all 12 with "Ion". Things are scripted, so it would be really nice
>> to be able to do that without additional indexing.
>>
>>
> Update residuetypes.dat to include your new ions.
>
> -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.thelemkullab.com
>
> ==
>
> --
> 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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Re: [gmx-users] Metal organic framework energy minimization

2018-07-25 Thread Lakshman Ji Verma

Based on these figures it appears that bonds are breaking which means they
are not defined correctly in your topology file.
Based on my experience, you might want to look in your .rtp file and ZIF
gro/pdb file and check the sequence of the atoms. All three files must have
the same sequence of atoms given that bonds are correct defined.

Thanks!
Lakshman

On Wed, Jul 25, 2018 at 2:53 PM Jordan Chapman 
wrote:

> Certainly, see the link below. The images should be clearly labeled.
> Solvent molecules are hidden for ease of viewing.
>
> https://www.dropbox.com/sh/td7gjj7cwmgsm6m/AAAoSzBdyzh4A7Ij6NTMlnmya?dl=0
>
> Jordan
>
> On Wed, Jul 25, 2018 at 3:08 PM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you can share some links to before and after images on a file sharing
> > service, then perhaps someone can suggest what the issue is. I don't
> follow
> > your description so far.
> >
> > Mark
> >
> > On Wed, Jul 25, 2018, 15:33 Jordan Chapman 
> wrote:
> >
> > > GROMACS users,
> > >
> > > I am attempting pre-processing of a metal organic framework (ZIF-8) in
> > > water, but I am running into trouble with energy minimization. I've
> added
> > > both bonded and nonbonded forcefield parameters for ZIF-8 into the
> > AMBER03
> > > forcefield library and solvated the system with the TIP3P water model
> > using
> > > "gmx solvate". The steepest descent algorithm converges to the options
> I
> > > have set in my minimization mdp file, and an analysis of potential
> energy
> > > over the simulation time using "gmx energy" follows an expected trend.
> > > However the simulation returns a warning that at several time steps in
> > the
> > > minimization one or more water molecules could not be settled.
> > >
> > > Depending on the size of the system I defined using "gmx editconf" I
> find
> > > that the ZIF-8 molecule by the end of the simulation is either crumpled
> > > when the box size is too large or stretched to the dimensions of the
> box
> > > when the box size is too small. For reference, the size of a unit cell
> of
> > > ZIF-8 is approximately 1.7 nm x 1.7 nm x 1.7 nm.
> > >
> > > I've analyzed the range of box dimensions that return either crumpled
> or
> > > stretched ZIF-8 conformations. At a diameter of 3.09 nm, energy
> > > minimization returns a stretched ZIF-8 structure. At a diameter of
> 3.0925
> > > nm, energy minimization returns a crumpled ZIF-8 structure. See below
> for
> > > the mdp options I have set for energy minimization. Energy minimization
> > of
> > > ZIF-8 at the same mdp options was successful for ZIF-8 in vacuum.
> > >
> > > ; Energy minimization of ZIF-8 unit cell in TIP3P
> > > include  =
> > > define   = -DPOSRES
> > >
> > > ; RUN CONTROL PARAMETERS
> > > integrator   = steep
> > > dt   = 0.001
> > > nsteps   = 10
> > > comm-mode= Linear
> > > nstcomm  = 20
> > > comm-grps=
> > >
> > >
> > > ; ENERGY MINIMIZATION OPTIONS
> > > emtol= 10
> > > emstep   = 0.01
> > >
> > >
> > > ; OUTPUT CONTROL OPTIONS
> > > nstxout  = 200
> > > nstvout  = 200
> > > nstfout  = 200
> > > nstlog   = 200
> > > nstcalcenergy= 200
> > > nstenergy= 200
> > > nstxout-compressed   = 0
> > > energygrps   =
> > >
> > >
> > > ; NEIGHBORSEARCHING PARAMETERS
> > > cutoff-scheme= Verlet
> > > nstlist  = 40
> > > ns_type  = grid
> > > pbc  = xyz
> > > periodic-molecules   = yes
> > > verlet-buffer-tolerance  = 0.0001
> > > rlist= 1.4
> > >
> > >
> > > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > > coulombtype  = PME
> > > coulomb-modifier =
> > > rcoulomb = 1.4
> > > vdwtype  = Cut-off
> > > vdw-modifier =
> > > rvdw = 1.4
> > > DispCorr = EnerPres
> > > ; EWALD/PME/PPPM parameters
> > > fourierspacing   = 0.12
> > > pme_order= 4
> > > ewald_rtol   = 1e-05
> > >
> > >
> > > ; GENERATE VELOCITIES FOR STARTUP RUN
> > > gen-vel  = no
> > > gen-temp = 300
> > > gen-seed = 3532
> > >
> > >
> > > ; OPTIONS FOR BONDS
> > > constraints  = none
> > >
> > > Any advice or insight into what could be causing this or a
> recommendation
> > > for appropriate pre-processing is greatly appreciated!
> > >
> > > Best,
> > > Jordan Chapman
> > > Graduate Research Assistant
> > > Department of Chemical and Biomedical Enginering
> > > West Virginia Univesity
> > > --
> > > 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

Re: [gmx-users] Metal organic framework energy minimization

2018-07-25 Thread Lakshman Ji Verma

On Wed, Jul 25, 2018 at 8:32 AM Jordan Chapman 
wrote:

> GROMACS users,
>
> I am attempting pre-processing of a metal organic framework (ZIF-8) in
> water, but I am running into trouble with energy minimization. I've added
> both bonded and nonbonded forcefield parameters for ZIF-8 into the AMBER03
> forcefield library and solvated the system with the TIP3P water model using
> "gmx solvate". The steepest descent algorithm converges to the options I
> have set in my minimization mdp file, and an analysis of potential energy
> over the simulation time using "gmx energy" follows an expected trend.
> However the simulation returns a warning that at several time steps in the
> minimization one or more water molecules could not be settled.
>

I have come across these errors. Apparently in my cases, water atoms
overlap with the other molecule. It happens because when we add water
molecules with gmx solvate, water molecules are added in all the possible
vacant spaces and some water molecules are added within molecules where
they are not supposed to be. So, I think water molecules in your case are
being inserted within the ZIF-8 framework where there is not enough space.
You might want to look at your input .gro file for minimization and remove
those water molecules.



> Depending on the size of the system I defined using "gmx editconf" I find
> that the ZIF-8 molecule by the end of the simulation is either crumpled
> when the box size is too large or stretched to the dimensions of the box
> when the box size is too small. For reference, the size of a unit cell of
> ZIF-8 is approximately 1.7 nm x 1.7 nm x 1.7 nm.
>

If bonds are breaking. You might want to look at bonds and dihedral angles
in your topology file and see if all the atoms are  connected correctly.

Thanks!
Lakshman


> I've analyzed the range of box dimensions that return either crumpled or
> stretched ZIF-8 conformations. At a diameter of 3.09 nm, energy
> minimization returns a stretched ZIF-8 structure. At a diameter of 3.0925
> nm, energy minimization returns a crumpled ZIF-8 structure. See below for
> the mdp options I have set for energy minimization. Energy minimization of
> ZIF-8 at the same mdp options was successful for ZIF-8 in vacuum.
>
> ; Energy minimization of ZIF-8 unit cell in TIP3P
> include  =
> define   = -DPOSRES
>
> ; RUN CONTROL PARAMETERS
> integrator   = steep
> dt   = 0.001
> nsteps   = 10
> comm-mode= Linear
> nstcomm  = 20
> comm-grps=
>
>
> ; ENERGY MINIMIZATION OPTIONS
> emtol= 10
> emstep   = 0.01
>
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 200
> nstvout  = 200
> nstfout  = 200
> nstlog   = 200
> nstcalcenergy= 200
> nstenergy= 200
> nstxout-compressed   = 0
> energygrps   =
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> cutoff-scheme= Verlet
> nstlist  = 40
> ns_type  = grid
> pbc  = xyz
> periodic-molecules   = yes
> verlet-buffer-tolerance  = 0.0001
> rlist= 1.4
>
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = PME
> coulomb-modifier =
> rcoulomb = 1.4
> vdwtype  = Cut-off
> vdw-modifier =
> rvdw = 1.4
> DispCorr = EnerPres
> ; EWALD/PME/PPPM parameters
> fourierspacing   = 0.12
> pme_order= 4
> ewald_rtol   = 1e-05
>
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen-vel  = no
> gen-temp = 300
> gen-seed = 3532
>
>
> ; OPTIONS FOR BONDS
> constraints  = none
>
> Any advice or insight into what could be causing this or a recommendation
> for appropriate pre-processing is greatly appreciated!
>
> Best,
> Jordan Chapman
> Graduate Research Assistant
> Department of Chemical and Biomedical Enginering
> West Virginia Univesity
> --
> 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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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] grouping custom ions


I knew there would have to be something like that!

Thanks a bunch,

Alex


On 7/25/2018 2:36 PM, Justin Lemkul wrote:



On 7/25/18 4:35 PM, Alex wrote:

Hi all,

Perhaps a trivial question here. I added a few custom metal ions into 
oplsaa's 'ions.itp' and 'ffnonbonded.itp' -- everything works fine. 
There is, however, a problem with selecting them in e.g. trjconv 
without using a custom index. Example: 5 NA, 6 CL, and 1 XX (custom) 
ions in the system. The group "Ion" now only contains 11 elements (NA 
+ CL), while I'd like to select all 12 with "Ion". Things are 
scripted, so it would be really nice to be able to do that without 
additional indexing.




Update residuetypes.dat to include your new ions.

-Justin



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Re: [gmx-users] grouping custom ions





On 7/25/18 4:35 PM, Alex wrote:

Hi all,

Perhaps a trivial question here. I added a few custom metal ions into 
oplsaa's 'ions.itp' and 'ffnonbonded.itp' -- everything works fine. 
There is, however, a problem with selecting them in e.g. trjconv 
without using a custom index. Example: 5 NA, 6 CL, and 1 XX (custom) 
ions in the system. The group "Ion" now only contains 11 elements (NA 
+ CL), while I'd like to select all 12 with "Ion". Things are 
scripted, so it would be really nice to be able to do that without 
additional indexing.




Update residuetypes.dat to include your new ions.

-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.thelemkullab.com

==

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[gmx-users] grouping custom ions


Hi all,

Perhaps a trivial question here. I added a few custom metal ions into 
oplsaa's 'ions.itp' and 'ffnonbonded.itp' -- everything works fine. 
There is, however, a problem with selecting them in e.g. trjconv without 
using a custom index. Example: 5 NA, 6 CL, and 1 XX (custom) ions in the 
system. The group "Ion" now only contains 11 elements (NA + CL), while 
I'd like to select all 12 with "Ion". Things are scripted, so it would 
be really nice to be able to do that without additional indexing.


Thanks!

Alex

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Re: [gmx-users] Metal organic framework energy minimization

2018-07-25 Thread Jordan Chapman

Certainly, see the link below. The images should be clearly labeled.
Solvent molecules are hidden for ease of viewing.

https://www.dropbox.com/sh/td7gjj7cwmgsm6m/AAAoSzBdyzh4A7Ij6NTMlnmya?dl=0

Jordan

On Wed, Jul 25, 2018 at 3:08 PM Mark Abraham 
wrote:

> Hi,
>
> If you can share some links to before and after images on a file sharing
> service, then perhaps someone can suggest what the issue is. I don't follow
> your description so far.
>
> Mark
>
> On Wed, Jul 25, 2018, 15:33 Jordan Chapman  wrote:
>
> > GROMACS users,
> >
> > I am attempting pre-processing of a metal organic framework (ZIF-8) in
> > water, but I am running into trouble with energy minimization. I've added
> > both bonded and nonbonded forcefield parameters for ZIF-8 into the
> AMBER03
> > forcefield library and solvated the system with the TIP3P water model
> using
> > "gmx solvate". The steepest descent algorithm converges to the options I
> > have set in my minimization mdp file, and an analysis of potential energy
> > over the simulation time using "gmx energy" follows an expected trend.
> > However the simulation returns a warning that at several time steps in
> the
> > minimization one or more water molecules could not be settled.
> >
> > Depending on the size of the system I defined using "gmx editconf" I find
> > that the ZIF-8 molecule by the end of the simulation is either crumpled
> > when the box size is too large or stretched to the dimensions of the box
> > when the box size is too small. For reference, the size of a unit cell of
> > ZIF-8 is approximately 1.7 nm x 1.7 nm x 1.7 nm.
> >
> > I've analyzed the range of box dimensions that return either crumpled or
> > stretched ZIF-8 conformations. At a diameter of 3.09 nm, energy
> > minimization returns a stretched ZIF-8 structure. At a diameter of 3.0925
> > nm, energy minimization returns a crumpled ZIF-8 structure. See below for
> > the mdp options I have set for energy minimization. Energy minimization
> of
> > ZIF-8 at the same mdp options was successful for ZIF-8 in vacuum.
> >
> > ; Energy minimization of ZIF-8 unit cell in TIP3P
> > include  =
> > define   = -DPOSRES
> >
> > ; RUN CONTROL PARAMETERS
> > integrator   = steep
> > dt   = 0.001
> > nsteps   = 10
> > comm-mode= Linear
> > nstcomm  = 20
> > comm-grps=
> >
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > emtol= 10
> > emstep   = 0.01
> >
> >
> > ; OUTPUT CONTROL OPTIONS
> > nstxout  = 200
> > nstvout  = 200
> > nstfout  = 200
> > nstlog   = 200
> > nstcalcenergy= 200
> > nstenergy= 200
> > nstxout-compressed   = 0
> > energygrps   =
> >
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > cutoff-scheme= Verlet
> > nstlist  = 40
> > ns_type  = grid
> > pbc  = xyz
> > periodic-molecules   = yes
> > verlet-buffer-tolerance  = 0.0001
> > rlist= 1.4
> >
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > coulombtype  = PME
> > coulomb-modifier =
> > rcoulomb = 1.4
> > vdwtype  = Cut-off
> > vdw-modifier =
> > rvdw = 1.4
> > DispCorr = EnerPres
> > ; EWALD/PME/PPPM parameters
> > fourierspacing   = 0.12
> > pme_order= 4
> > ewald_rtol   = 1e-05
> >
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen-vel  = no
> > gen-temp = 300
> > gen-seed = 3532
> >
> >
> > ; OPTIONS FOR BONDS
> > constraints  = none
> >
> > Any advice or insight into what could be causing this or a recommendation
> > for appropriate pre-processing is greatly appreciated!
> >
> > Best,
> > Jordan Chapman
> > Graduate Research Assistant
> > Department of Chemical and Biomedical Enginering
> > West Virginia Univesity
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Protein surface interaction analysis - hydrophobic sasa

Hi,

Which groups Sasa are you trying to measure?

Mark

On Wed, Jul 25, 2018, 12:16 Milan Sobota  wrote:

> Dear gromacs users,
>
> I am simulating the binding of a peptide to a hydrophobic polymer surface
> (100 short polymer chains arranged in a brush like layer). I want to
> calculate the hydrophobic and hydrophilic sasa seperately, as well as the
> contact area, which should be the decrease in hydrophobic sasa upon
> binding. To do this, I ran:
> gmx sasa -surface 'group "non-Water"' -output '"Hydrophobic" group
> "non-Water" and charge {-0.2 to 0.2}; "Hydrophilic" group "Protein" and not
> charge {-0.2 to 0.2}; "Total" group "Protein"'
> as described at
>
> http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas
>
> Is this the right approach, or what would be the right one? Does this count
> the hydrophobic contact area twice for my case, since I have more than just
> protein in the "non-water" group?
>
> Additionally, I am using g_mmpbsa and gmx mindist to calculate binding
> energies and contact timelines. Are there other ways to analyze this type
> of interaction that I should be aware of?
>
> Thanks and kind regards,
>
> Milan H B Sobota
> RWTH Aachen University
> --
> Gromacs Users mailing list
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Re: [gmx-users] Energy decomposition

Hi,

On Tue, Jul 24, 2018, 12:33 Vito GENNA  wrote:

> Dear all,
>
> I have followed the procedure you have suggested.
> Now I have a trajectory only containing my selected atoms and its related
> .tpr file.
> However, after running g_energy and selecting "total energy" I get an
> energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol).
> I feel something is going wrong. Have you got any idea?
>

No. What value would be appropriate, and why?

Furthermore, if I would decompose this total energy in bond term, stretch
> term, angle term etc etc, which would be the best way to do it?
>

You can edit the topology before you give it to grompp if the default
decomposition isn't suitable for you. But I know of no use for such a
decomposition, nor a force field that was parameterized with such a use
case in mind.

Mark

Thanks in advance for your contribute.
>
> V
>
> On Sun, Jul 8, 2018 at 8:17 PM, Vito GENNA 
> wrote:
>
> > Dear Justin,
> >
> > Thanks a lot.
> > I indeed did not consider the idea to extrapolate only a part of the
> whole
> > trajectory. Nice shot.
> > Well, regarding the forcefield, this calculation in part is aiming to a
> > kind of “ff validation”.
> >
> > Thanks a lot for your prompt reply.
> >
> > V
> >
> > *Vito Genna, Ph.D*
> > PostDoctoral Researcher
> > Molecular Modelling and Bioinformatics
> > Orozco Lab
> >
> > *Dep. of Structural and Computational Biology*
> > *Institute for Research in Biomedicine (IRB Barcelona)*
> > Parc Científic de
> 
> Barcelona
> > C/ Baldiri Reixac 10-12
> > 08028 Barcelona
> >
> > P.S. This message has been written with my IPhone. Sorry for typo.
> >
> > Il giorno 08 lug 2018, alle ore 20:12, Justin Lemkul 
> ha
> > scritto:
> >
> >
> >
> > On 7/8/18 2:06 PM, Vito GENNA wrote:
> >
> > Dear GMXusers,
> >
> >
> > I am writing you in the hope to find a solution to my problem.
> >
> >
> > I'd love (and truly love) calculate the intramolecular energy (both
> bonded
> >
> > and non-bonded terms) of a DNA backbone for which I have a .xtc
> trajectory
> >
> > (and of course coords).
> >
> >
> > What I did:
> >
> >
> > 1) defined the index.ndx for each DNA strand and generated a ndx.file
> >
> > cotaining [strand-1] and [System - (strand-1)] (works fine)
> >
> >
> > 2) Changed the energygrps in the mdp file to: [strand-1]  [System -
> >
> > (strand-1)] (works fine)
> >
> >
> > 3) Generated a .tpr file selecting (from point 1) the .ndx of my interest
> >
> >
> > 4) with mdrun with -rerun option (by using the .tpr of my interest
> >
> > generated at the previous stage) I get the .edr file [strand-1]
> >
> >
> > 5) by using g_energy I only get Lennard-Jones and Coulomb terms (both
> short
> >
> > and long for [strand-1]:[strand-1]) while I would also include the
> >
> > bonded-terms.
> >
> >
> > 6) The option ETOT, provided by g_energy, I guess does not return the E
> of
> >
> > the strand, rather of the overall system. Isn't it?
> >
> >
> > Since I am comparing the same system in different conditions (then in
> >
> > different MD) I am looking for a strategy which would allow me to
> >
> > extrapolate all the energy terms for the backbone in a consistent
> fashion.
> >
> >
> > Did you ever calculated something similar?
> >
> > If so, how?
> >
> >
> > You need to extract only the coordinates you want from the trajectory
> with
> > trjconv and your index group. Then, create a matching .tpr file with only
> > those atoms using convert-tpr. Then use mdrun -rerun. Whether or not the
> > quantity means anything depends on how your force field was parametrized,
> > but that's how you calculate it.
> >
> > -Justin
> >
> > If not, any suggestion?
> >
> >
> > Thanks in advance for all your comments.
> >
> >
> > All the Best
> >
> >
> > VG
> >
> >
> > PS: Gromacs version: 5.0.4
> >
> >
> >
> > --
> > ==
> >
> > 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.thelemkullab.com
> >
> > ==
> >
> > --
> > 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.
> >
> >
>
>
> --
>
> ***
> *Vito Genna, Ph.D*
>
> *Postoctoral Researcher*
>
> *Molecular Modeling and Bioinformatics*
> *Orozco Lab*
>
> *Institute for Research in Biomedicine (IRB Barcelona)*
>
> *Parc Centific de Barcelona*
>
> *C/ Baldiri Reixac 10-12*
> *08028 Barcelona*
>
>

Re: [gmx-users] Metal organic framework energy minimization

Hi,

If you can share some links to before and after images on a file sharing
service, then perhaps someone can suggest what the issue is. I don't follow
your description so far.

Mark

On Wed, Jul 25, 2018, 15:33 Jordan Chapman  wrote:

> GROMACS users,
>
> I am attempting pre-processing of a metal organic framework (ZIF-8) in
> water, but I am running into trouble with energy minimization. I've added
> both bonded and nonbonded forcefield parameters for ZIF-8 into the AMBER03
> forcefield library and solvated the system with the TIP3P water model using
> "gmx solvate". The steepest descent algorithm converges to the options I
> have set in my minimization mdp file, and an analysis of potential energy
> over the simulation time using "gmx energy" follows an expected trend.
> However the simulation returns a warning that at several time steps in the
> minimization one or more water molecules could not be settled.
>
> Depending on the size of the system I defined using "gmx editconf" I find
> that the ZIF-8 molecule by the end of the simulation is either crumpled
> when the box size is too large or stretched to the dimensions of the box
> when the box size is too small. For reference, the size of a unit cell of
> ZIF-8 is approximately 1.7 nm x 1.7 nm x 1.7 nm.
>
> I've analyzed the range of box dimensions that return either crumpled or
> stretched ZIF-8 conformations. At a diameter of 3.09 nm, energy
> minimization returns a stretched ZIF-8 structure. At a diameter of 3.0925
> nm, energy minimization returns a crumpled ZIF-8 structure. See below for
> the mdp options I have set for energy minimization. Energy minimization of
> ZIF-8 at the same mdp options was successful for ZIF-8 in vacuum.
>
> ; Energy minimization of ZIF-8 unit cell in TIP3P
> include  =
> define   = -DPOSRES
>
> ; RUN CONTROL PARAMETERS
> integrator   = steep
> dt   = 0.001
> nsteps   = 10
> comm-mode= Linear
> nstcomm  = 20
> comm-grps=
>
>
> ; ENERGY MINIMIZATION OPTIONS
> emtol= 10
> emstep   = 0.01
>
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 200
> nstvout  = 200
> nstfout  = 200
> nstlog   = 200
> nstcalcenergy= 200
> nstenergy= 200
> nstxout-compressed   = 0
> energygrps   =
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> cutoff-scheme= Verlet
> nstlist  = 40
> ns_type  = grid
> pbc  = xyz
> periodic-molecules   = yes
> verlet-buffer-tolerance  = 0.0001
> rlist= 1.4
>
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = PME
> coulomb-modifier =
> rcoulomb = 1.4
> vdwtype  = Cut-off
> vdw-modifier =
> rvdw = 1.4
> DispCorr = EnerPres
> ; EWALD/PME/PPPM parameters
> fourierspacing   = 0.12
> pme_order= 4
> ewald_rtol   = 1e-05
>
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen-vel  = no
> gen-temp = 300
> gen-seed = 3532
>
>
> ; OPTIONS FOR BONDS
> constraints  = none
>
> Any advice or insight into what could be causing this or a recommendation
> for appropriate pre-processing is greatly appreciated!
>
> Best,
> Jordan Chapman
> Graduate Research Assistant
> Department of Chemical and Biomedical Enginering
> West Virginia Univesity
> --
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Re: [gmx-users] specbond

Hi,

Normally rtp entries specify the bonds and all the angles are inferred and
the parameters for everything are deduced from atom types. That's the same
with bonds that originated from specbonds.dat entries.

Note that if the MOF has head to tail bonding then you can use the same
mechanism as the protein force fields use, with + and - notations (see docs
and the examples in aminoacids.rtp).

Mark

On Wed, Jul 25, 2018, 17:14 Momin Ahmad  wrote:

> Hello,
>
> i parametrized two component of my metal-organic framework as modular
> building block. Each component has an entry in the .rtp file and pdb2gmx
> and grompp do work. Now i want to define bonds between both residues. In
> specbond.dat it is possible to do so but where do i put in the new
> force-field parameters for additional bonds, angles, dihedrals that are
> formed by the intermolecular bond?
>
> Kind regards
> 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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[gmx-users] specbond

2018-07-25 Thread Momin Ahmad


Hello,

i parametrized two component of my metal-organic framework as modular 
building block. Each component has an entry in the .rtp file and pdb2gmx 
and grompp do work. Now i want to define bonds between both residues. In 
specbond.dat it is possible to do so but where do i put in the new 
force-field parameters for additional bonds, angles, dihedrals that are 
formed by the intermolecular bond?


Kind regards
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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Re: [gmx-users] OpenMP multithreading mdrun

2018-07-25 Thread Szilárd Páll

On Wed, Jul 25, 2018 at 4:27 PM Smith, Iris  wrote:

> Good Morning Gromacs Users,
>
> Gromacs 2018.2 was recently installed on our intel-based HPC cluster using
> OpenMP (without MPI).
>
> Can I still utilize multiple threads within one node when utilizing mdrun?
> If so, do I need to call openmp and export OMP_NUM_THREADS in my script?
>

OpenMP enables multi-threading within mdrun, so yes, you can. Unless it's
been disabled, you can also use the built-in therads-based MPI (called
thread-MPI); see:
http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node


> For example when using 20 threads:
>
> module load openmpi/gcc/64/3.1.1
> module load gromacs/2018.2
> export OMP_NUM_THREADS=2
>
> gmx mdrun -ntomp 20 -s wt.tpr -deffnm wt -v
>

-ntomp and OMP_NUM_THREADS are synonymous; it's enough if you set either,
but if you set both you have to set them to identical values, the above
will not work.

--
Szilárd


>
> Thank you,
> Iris
>
>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1326358176]
>
> Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
> Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  |
> (216) 445-7885
>
>
>
>
> ===
>
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
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[gmx-users] OpenMP multithreading mdrun

2018-07-25 Thread Smith, Iris

Good Morning Gromacs Users,

Gromacs 2018.2 was recently installed on our intel-based HPC cluster using
OpenMP (without MPI).

Can I still utilize multiple threads within one node when utilizing mdrun? If
so, do I need to call openmp and export OMP_NUM_THREADS in my script?

For example when using 20 threads:

module load openmpi/gcc/64/3.1.1
module load gromacs/2018.2
export OMP_NUM_THREADS=2

gmx mdrun -ntomp 20 -s wt.tpr -deffnm wt -v

Thank you,
Iris

[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1326358176]

===

Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by
U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services, staff
and locations. Confidentiality Note: This message is intended for use only by
the individual or entity to which it is addressed and may contain information
that is privileged, confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended recipient or the
employee or agent responsible for delivering the message to the intended
recipient, you are hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If you have received this
communication in error, please contact the sender immediately and destroy the
material in its entirety, whether electronic or hard copy. Thank you.
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[gmx-users] Metal organic framework energy minimization

2018-07-25 Thread Jordan Chapman

GROMACS users,

I am attempting pre-processing of a metal organic framework (ZIF-8) in
water, but I am running into trouble with energy minimization. I've added
both bonded and nonbonded forcefield parameters for ZIF-8 into the AMBER03
forcefield library and solvated the system with the TIP3P water model using
"gmx solvate". The steepest descent algorithm converges to the options I
have set in my minimization mdp file, and an analysis of potential energy
over the simulation time using "gmx energy" follows an expected trend.
However the simulation returns a warning that at several time steps in the
minimization one or more water molecules could not be settled.

Depending on the size of the system I defined using "gmx editconf" I find
that the ZIF-8 molecule by the end of the simulation is either crumpled
when the box size is too large or stretched to the dimensions of the box
when the box size is too small. For reference, the size of a unit cell of
ZIF-8 is approximately 1.7 nm x 1.7 nm x 1.7 nm.

I've analyzed the range of box dimensions that return either crumpled or
stretched ZIF-8 conformations. At a diameter of 3.09 nm, energy
minimization returns a stretched ZIF-8 structure. At a diameter of 3.0925
nm, energy minimization returns a crumpled ZIF-8 structure. See below for
the mdp options I have set for energy minimization. Energy minimization of
ZIF-8 at the same mdp options was successful for ZIF-8 in vacuum.

; Energy minimization of ZIF-8 unit cell in TIP3P
include  =
define   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator   = steep
dt   = 0.001
nsteps   = 10
comm-mode= Linear
nstcomm  = 20
comm-grps=


; ENERGY MINIMIZATION OPTIONS
emtol= 10
emstep   = 0.01


; OUTPUT CONTROL OPTIONS
nstxout  = 200
nstvout  = 200
nstfout  = 200
nstlog   = 200
nstcalcenergy= 200
nstenergy= 200
nstxout-compressed   = 0
energygrps   =


; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme= Verlet
nstlist  = 40
ns_type  = grid
pbc  = xyz
periodic-molecules   = yes
verlet-buffer-tolerance  = 0.0001
rlist= 1.4


; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
coulomb-modifier =
rcoulomb = 1.4
vdwtype  = Cut-off
vdw-modifier =
rvdw = 1.4
DispCorr = EnerPres
; EWALD/PME/PPPM parameters
fourierspacing   = 0.12
pme_order= 4
ewald_rtol   = 1e-05


; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel  = no
gen-temp = 300
gen-seed = 3532


; OPTIONS FOR BONDS
constraints  = none

Any advice or insight into what could be causing this or a recommendation
for appropriate pre-processing is greatly appreciated!

Best,
Jordan Chapman
Graduate Research Assistant
Department of Chemical and Biomedical Enginering
West Virginia Univesity
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Re: [gmx-users] mpirun and gmx_mpi

2018-07-25 Thread Szilárd Páll

On Wed, Jul 25, 2018 at 1:43 PM Mahmood Naderan 
wrote:

> It is stated that
>
>
> mpirun -np 4 gmx mdrun -ntomp 6 -nb gpu -gputasks 00
>
> Starts gmx mdrun
> 
> on a machine with two nodes, using four total ranks, each rank with six
> OpenMP threads, and both ranks on a node sharing GPU with ID 0.
>
>
>
> Questions are:
>
> 1- Why gmx_mpi is not used?
>

Though not wrong, that's a typo, the default binary suffix of MPI builds is
"_mpi", but it can be changed:
http://manual.gromacs.org/documentation/2018/install-guide/index.html#changing-the-names-of-gromacs-binaries-and-libraries

>
> 2- How two nodes were specified in the command line?
>

The way you launch an MPI program on multiple nodes is specific to the
cluster setup and not specific to GROMACS. For the details of how you
launch MPI programs on the hardware you have access to, you need to consult
the documentation of your cluster.

>
> 3- Total four ranks and two ranks on GPU?!
>

Yes. What is the question?

4- Is that using Nvidia MPS? Due to the single GPU device which is shared
> between ranks.
>

If you use MPS on the compute nodes, it will use MPS. If you don't,
processes will share GPUs, but execution will be somewhat less efficient.

--
Szilárd

>
>
> Regards,
> Mahmood
>
>
> On Wednesday, July 25, 2018, 1:05:10 AM GMT+4:30, Szilárd Páll <
> pall.szil...@gmail.com> wrote:
>
>
> That choice depends on whether you want to run across multiple compute
> nodes; the former can not while the latter, as it is (by default) indicates
> that it's using an MPI library, can run across nodes. Both can be used on
> GPUs as long as the programs were built with GPU support.
>
> I recommend that you check the documentation:
>
> http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node
>
> --
> Szilárd
>
>
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Re: [gmx-users] energy minimization

2018-07-25 Thread Smith, Micholas D.

LigParGen generates new atom types for each ligand topology it generates. The 
output files from LigParGen should contain terms for opls800-925 (if necessary) 
in the generated topology file. These need to be included in the force-field 
file you use for use in your simulations. 

A warning should be made about LigParGen: each atom is given a unique atomtype. 
For instance if you have a 25 atom ligand, you will have atomtypes opls 800 
through opls824. Some of these may be repeats. This means that if you want to 
run with a different ligand you have to change these atomtype definitions each 
time.

Hope that helps.

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

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

Sent: Wednesday, July 25, 2018 8:17 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization

On 7/24/18 7:24 AM, farial tavakoli wrote:
> Dear Justin
>
> I used LigParGen server to generate ligand topology but I dont know what 
> changes I have to do in .itp file.
>   when I issued this command:
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor
>
> faced this error:ERROR 1 [file LIG.itp, line 11]:
>Atomtype opls_800 not found
> I checked the aminoacids.rtp file  of  
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not 
> atomtype opls_800 and 801 and ... in this file. while the LIG.itp which 
> generated by LigParGen server has atomtype opls_800 , 801 and ... .
> I have to modify all of these atomtype opls_ in order to correspond to with 
> aminoacid.rtp file?
> I would be thankfull if you help me.
> bestFraial

It looks like your topology introduces new atom types. Check the
LigParGen documentation to see if it requires a different version of the
force field or if the parameters are provided somewhere.

-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.thelemkullab.com

==

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Re: [gmx-users] energy minimization




On 7/24/18 7:24 AM, farial tavakoli wrote:

Dear Justin

I used LigParGen server to generate ligand topology but I dont know what 
changes I have to do in .itp file.
  when I issued this command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor

faced this error:ERROR 1 [file LIG.itp, line 11]:
   Atomtype opls_800 not found
I checked the aminoacids.rtp file  of  
/usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype 
opls_800 and 801 and ... in this file. while the LIG.itp which generated by 
LigParGen server has atomtype opls_800 , 801 and ... .
I have to modify all of these atomtype opls_ in order to correspond to with 
aminoacid.rtp file?
I would be thankfull if you help me.
bestFraial


It looks like your topology introduces new atom types. Check the 
LigParGen documentation to see if it requires a different version of the 
force field or if the parameters are provided somewhere.


-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.thelemkullab.com

==

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Re: [gmx-users] topol inaccessible in the production md step





On 7/25/18 7:24 AM, Raag Saluja wrote:

Hi!

I'm simulating a heterodimer, with the help of your lysoyme tutorial. The
simulation runs smoothly till the production MD step.

I gave these commands:

gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr

time -p mpirun gmx_mpi mdrun -v -deffnm md

I kept md.mdp identical to the one given in the tutorial, except that I
changed the number of steps to 2500.

I got an error saying that 'topol' was inaccessible or didn't exist. The
topol file is very much there and all the previous commands worked. Where
am I going wrong?


Your naming is inconsistent. You made a .tpr file called "md_0_1.tpr" 
and then you're asking mdrun to execute "md.tpr," which does not exist. 
Since mdrun cannot find "md.tpr," it looks for the default file name, 
"topol.tpr," which it also doesn't find. Hence, you get a fatal error.


-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.thelemkullab.com

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[gmx-users] xdrfile library problem on Ubuntu 18.04 LTS

2018-07-25 Thread Геннадий Макаров


Dear GROMACS users and developers,


I have problem with xdrfile library during reading *.xtc from python scripts. A 
month ago operating system of collectively used computer was upgraded from 
Ubuntu 12.04 LTS to Ubuntu 18.04 LTS. Since this, xdrfile library do not work 
even it was re-compiled. 


Debugging with GDB reveals segmentation fault on lines 267 and 279 of 
xdrfile.c: 
==
Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x7fffb805ff49 in xdrfile_read_int (ptr=0x7fffcf1c, ndata=1, 
xfp=0x55f7e240) at xdrfile.c:267
267 while(ixdr),ptr+i))
==
Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x7fffb805ff9d in xdrfile_write_int (ptr=0x7fffd0a8, ndata=1, 
xfp=0x55e5abf0) at xdrfile.c:279
279 while(ixdr),ptr+i))

==

This phenomenon is present for any *.xtc file and for libxdrfile.so compiled by 
GCC 4.4, 4.6, 4.8 and 7.3. Help me please, because of this error I can not use 
my inhouse Python programs for analysis of trajectories.



Gennady Makarov
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Re: [gmx-users] mpirun and gmx_mpi

2018-07-25 Thread Mahmood Naderan

It is stated that 


mpirun -np 4 gmx mdrun -ntomp 6 -nb gpu -gputasks 00

Starts gmx mdrun on a machine with two nodes, usingfour total ranks, each rank 
with six OpenMP threads,and both ranks on a node sharing GPU with ID 0.



Questions are:
1- Why gmx_mpi is not used?
2- How two nodes were specified in the command line?
3- Total four ranks and two ranks on GPU?!
4- Is that using Nvidia MPS? Due to the single GPU device which is shared 
between ranks.


Regards,
Mahmood 

On Wednesday, July 25, 2018, 1:05:10 AM GMT+4:30, Szilárd Páll 
 wrote:  

That choice depends on whether you want to run across multiple compute nodes; 
the former can not while the latter, as it is (by default) indicates that it's 
using an MPI library, can run across nodes. Both can be used on GPUs as long as 
the programs were built with GPU support. 

I recommend that you check the documentation:
http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node
--
Szilárd
  
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Re: [gmx-users] Energy decomposition

2018-07-25 Thread Vito GENNA

Dear all,

I have followed the procedure you have suggested.
Now I have a trajectory only containing my selected atoms and its related
.tpr file.
However, after running g_energy and selecting "total energy" I get an
energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol).
I feel something is going wrong. Have you got any idea?

Furthermore, if I would decompose this total energy in bond term, stretch
term, angle term etc etc, which would be the best way to do it?

Thanks in advance for your contribute.

V

On Sun, Jul 8, 2018 at 8:06 PM, Vito GENNA 
wrote:

> Dear GMXusers,
>
> I am writing you in the hope to find a solution to my problem.
>
> I'd love (and truly love) calculate the intramolecular energy (both bonded
> and non-bonded terms) of a DNA backbone for which I have a .xtc trajectory
> (and of course coords).
>
> What I did:
>
> 1) defined the index.ndx for each DNA strand and generated a ndx.file
> cotaining [strand-1] and [System - (strand-1)] (works fine)
>
> 2) Changed the energygrps in the mdp file to: [strand-1]  [System -
> (strand-1)] (works fine)
>
> 3) Generated a .tpr file selecting (from point 1) the .ndx of my interest
>
> 4) with mdrun with -rerun option (by using the .tpr of my interest
> generated at the previous stage) I get the .edr file [strand-1]
>
> 5) by using g_energy I only get Lennard-Jones and Coulomb terms (both
> short and long for [strand-1]:[strand-1]) while I would also include the
> bonded-terms.
>
> 6) The option ETOT, provided by g_energy, I guess does not return the E of
> the strand, rather of the overall system. Isn't it?
>
> Since I am comparing the same system in different conditions (then in
> different MD) I am looking for a strategy which would allow me to
> extrapolate all the energy terms for the backbone in a consistent fashion.
>
> Did you ever calculated something similar?
> If so, how?
> If not, any suggestion?
>
> Thanks in advance for all your comments.
>
> All the Best
>
> VG
>
> PS: Gromacs version: 5.0.4
>
> --
>
> ***
> *Vito Genna, Ph.D*
>
> *Postoctoral Researcher*
>
> *Molecular Modeling and Bioinformatics*
> *Orozco Lab*
>
> *Institute for Research in Biomedicine (IRB Barcelona)*
>
> *Parc Centific de Barcelona*
>
> *C/ Baldiri Reixac 10-12*
> *08028 Barcelona*
>
> ***
>

-- 

***
*Vito Genna, Ph.D*

*Postoctoral Researcher*

*Molecular Modeling and Bioinformatics*
*Orozco Lab*

*Institute for Research in Biomedicine (IRB Barcelona)*

*Parc Centific de Barcelona*

*C/ Baldiri Reixac 10-12*
*08028 Barcelona*

***
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[gmx-users] topol inaccessible in the production md step

2018-07-25 Thread Raag Saluja

Hi!

I'm simulating a heterodimer, with the help of your lysoyme tutorial. The
simulation runs smoothly till the production MD step.

I gave these commands:

gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr

time -p mpirun gmx_mpi mdrun -v -deffnm md

I kept md.mdp identical to the one given in the tutorial, except that I
changed the number of steps to 2500.

I got an error saying that 'topol' was inaccessible or didn't exist. The
topol file is very much there and all the previous commands worked. Where
am I going wrong?

Looking forward to your kind help!

Regards,
Raag
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[gmx-users] Protein surface interaction analysis - hydrophobic sasa

2018-07-25 Thread Milan Sobota

Dear gromacs users,

I am simulating the binding of a peptide to a hydrophobic polymer surface
(100 short polymer chains arranged in a brush like layer). I want to
calculate the hydrophobic and hydrophilic sasa seperately, as well as the
contact area, which should be the decrease in hydrophobic sasa upon
binding. To do this, I ran:
gmx sasa -surface 'group "non-Water"' -output '"Hydrophobic" group
"non-Water" and charge {-0.2 to 0.2}; "Hydrophilic" group "Protein" and not
charge {-0.2 to 0.2}; "Total" group "Protein"'
as described at
http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas

Is this the right approach, or what would be the right one? Does this count
the hydrophobic contact area twice for my case, since I have more than just
protein in the "non-water" group?

Additionally, I am using g_mmpbsa and gmx mindist to calculate binding
energies and contact timelines. Are there other ways to analyze this type
of interaction that I should be aware of?

Thanks and kind regards,

Milan H B Sobota
RWTH Aachen University
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Re: [gmx-users] gmx density -d Z in a system with pbc = xy

Hi,

You don't want periodic imaging to affect which z coordinates are in which
bin, so you want a large range of z

Mark

On Wed, Jul 25, 2018, 09:42 Alex  wrote:

> Hi Mark,
> Thanks.
> You mean EITHER .tpr with XYZ periodicity OR a sufficiently large Z size
> without periodicity in the Z direction?
> Because with pbc = xyz doesn’t matter how large is the box in Z direction.
> Regards,
> Alex
>
> On Wed, Jul 25, 2018 at 02:17 Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Maybe that's a limitation of gmx density. Make an equivalent .tpr with
> XYZ
> > periodicity and a sufficiently large z size.
> >
> > Mark
> >
> > On Tue, Jul 24, 2018, 22:52 Alex  wrote:
> >
> > > I have pbc only in X-Y directions in my simulations (pbc = xy), and I
> > want
> > > to calculate the number density in Z direction using the "gmx density
> -f
> > > *.xtc -s *.tpr -d Z -dens number" but the gmx density just stuck in the
> > > beginning. I wonder how I can density in Z direction in such
> situations?
> > > Thank you.
> > >
> > > Best regards,
> > > Alex
> > > --
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Re: [gmx-users] gmx density -d Z in a system with pbc = xy

Hi Mark,
Thanks.
You mean EITHER .tpr with XYZ periodicity OR a sufficiently large Z size
without periodicity in the Z direction?
Because with pbc = xyz doesn’t matter how large is the box in Z direction.
Regards,
Alex

On Wed, Jul 25, 2018 at 02:17 Mark Abraham  wrote:

> Hi,
>
> Maybe that's a limitation of gmx density. Make an equivalent .tpr with XYZ
> periodicity and a sufficiently large z size.
>
> Mark
>
> On Tue, Jul 24, 2018, 22:52 Alex  wrote:
>
> > I have pbc only in X-Y directions in my simulations (pbc = xy), and I
> want
> > to calculate the number density in Z direction using the "gmx density -f
> > *.xtc -s *.tpr -d Z -dens number" but the gmx density just stuck in the
> > beginning. I wonder how I can density in Z direction in such situations?
> > Thank you.
> >
> > Best regards,
> > Alex
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] pull COM code pullx.xvg vs gmx distance

2018-07-25 Thread Joe Wu

Hello,

I was wondering what the differences between pullx.xvg and gmx distance are.

"pullx.xvg" is the output of an umbrella sample mdrun.
"distance.xvg" is the output of this command (I am comparing the
z-component distance):

gmx distance -s umbrella01.tpr -f umbrella01.trr -oxyz dist.xvg -select
'com of group "Water" plus com of group "Ion"'

I did a pull of an ion on the +z axis through water solvent. Then, I did an
umbrella sample on 28 umbrella windows, each 0.05nm apart from distances 0
to 1.4nm. I am comparing the "pullx.xvg" and "distance.xvg" output of any
one of these windows, and it seems that for the most part, both z-distances
are the same (with a deviation of +/-0.001 due to sig-figs); however there
are a few time steps where the pullx distance deviates a lot from the
distance.xvg distance.

The pull portion of my MDP file is:

; Pull code

pull= yes

pull_ngroups= 2

pull_ncoords= 1

pull_group1_name= Water

pull_group2_name= Ion

pull_coord1_type= umbrella

pull_coord1_geometry= direction

pull_coord1_vec = 0 0 1

pull_coord1_groups  = 1 2

pull_coord1_dim = N N Y

pull_coord1_rate= 0.0

pull_coord1_k   = 4000

pull_coord1_start   = no

pull_coord1_init= 0.1

Does anyone know why these two z-component distances are not identical, as
they should? I am graphing both "pullx.xvg" and "distance.xvg" z-distance
as a function of time; both graphs should be superimposable, but they are
not. Why is this the case?

Please let me know if you need more information.

Thank you for your time!

Best,
Joe
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Re: [gmx-users] gmx density -d Z in a system with pbc = xy