Re: [gmx-users] What's new in GROMACS 2018? - a BioExcel webinar

[Rossen Apostolov]

Dear all,

For those who missed the event, a recording is available at

https://bioexcel.eu/webinar-gromacs-2018-overview-of-the-new-features-and-capabilities-2018-03-27/

Rossen


On 2018-03-26 11:25, Rossen Apostolov wrote:


Dear GROMACS users,

BioExcel CoE (https://bioexcel.eu) is organizing *tomorrow from 14:00 
GMT (15:00 CEST) *a webinar on the features, hardware support and 
various enhancements in the latest 2018 major release. At the end of 
the presentation, Mark Abraham, the GROMACS development manager, will 
answer your questions regarding the release.


You can register here: 
https://bioexcel.eu/webinar-gromacs-2018-overview-of-the-new-features-and-capabilities-2018-03-27/


Note that we have a limit of 100 attendees and there are already over 
50 registrants.


Rossen



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Re: [gmx-users] RDF brads

[Joe Jordan]

You can just give the selection you would use to make the ndx file directly
to gmx rdf.

You should be fine to average the simulations RDF (and e.g. PCA) are
statistical properties, and averaging should give you better statistics =)

On Wed, Mar 28, 2018 at 11:56 PM, Alex  wrote:

> Dear all,
>
> To obtain the coarse-graine (CG) parameters of a molecule using votca,
> below are the considered beads: (the bead are weighted by atomic weights )
> Bead A contains atoms of " a1, ..., a11"
> Bead B contains atoms of " b1, ..., b9"
> Bead C contains atoms of " c1,..., c13"
>
> Now, to calculate the RDF (A-A, A-B, A-C, B-C, B-B and C-C), in the all
> atom gromacs, would you please confirm me that I have to bundle the atoms
> of a1, ..., a11 in index.ndx (gmx make_ndx) in a section called A (and for
> the rest as well), and then using gmx rdf -ref A -sel B ... I am able to
> calculate a RDF similar to what I get in CG?
>
> One more question:
>
> Since the molecule which I was talking about in the last question is a log
> polymer which is hard to move and also I considered to have 300 molecules
> of that in my all atom MD system, so, I did not simulate my system for a
> long time (25 ns), but rather I simulated the system in multiple short MD
> simulation (5 * 5 ns), each with different initial conf.gro (but all
> include 300 molecules), now, I was wondering how can I calculate the
> physical quantities of the system out of those simulation? for example for
> the RDF, can I average the RDF of the 5 short simulations to get the final
> RDF?
>
> Thank you.
> Best regards,
> Alex
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[gmx-users] Parameters in top

[Dawid das]

Dear Gromacs Users,

If I have some bonding parameters defined in aminoacids.rtp instead of
ffbonded.itp
I noticed that these parameters appear in my topology *top file.

If I change these parameters in *top file but not in aminoacids.rtp, and
get new *trp file with grompp will my parameters also change? In other words
parameters in *top are taken as they are by Gromacs or still they are taken
from the force field files?

Best wishes,
Dawid
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Re: [gmx-users] Parameters in top

[Joe Jordan]

Perhaps this is a good chance for some testing or your part =)

On Thu, Mar 29, 2018 at 9:33 AM, Dawid das  wrote:

> Dear Gromacs Users,
>
> If I have some bonding parameters defined in aminoacids.rtp instead of
> ffbonded.itp
> I noticed that these parameters appear in my topology *top file.
>
> If I change these parameters in *top file but not in aminoacids.rtp, and
> get new *trp file with grompp will my parameters also change? In other
> words
> parameters in *top are taken as they are by Gromacs or still they are taken
> from the force field files?
>
> Best wishes,
> Dawid
> --
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> send a mail to gmx-users-requ...@gromacs.org.
>



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Joe Jordan
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Re: [gmx-users] Parameters in top

[Mark Abraham]

Hi,

The .rtp files are used by pdb2gmx, not grompp.

Mark

On Thu, Mar 29, 2018 at 9:33 AM Dawid das  wrote:

> Dear Gromacs Users,
>
> If I have some bonding parameters defined in aminoacids.rtp instead of
> ffbonded.itp
> I noticed that these parameters appear in my topology *top file.
>
> If I change these parameters in *top file but not in aminoacids.rtp, and
> get new *trp file with grompp will my parameters also change? In other
> words
> parameters in *top are taken as they are by Gromacs or still they are taken
> from the force field files?
>
> Best wishes,
> Dawid
> --
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Re: [gmx-users] Performance

[Szilárd Páll]

Thanks. Looks like the messages and error handling is somewhat
confusing; you must have the OMP_NUM_THREADS environment variable set
which (just as setting -ntomp), without setting -ntmpi too is not
supported.

Either let mdrun decide about the thread count or set -ntmpi manually.

--
Szilárd


On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi  wrote:
> Does it work?
>
> https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl
>
> How about this?
>
>
> Myunggi Yi
>
> On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Attachments can't be accepted on the list - please upload to a file sharing
>> service and share links to those.
>>
>> Mark
>>
>> On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi  wrote:
>>
>> > I am attaching the file.
>> >
>> > Thank you.
>> >
>> > Myunggi Yi
>> >
>> > On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll 
>> > wrote:
>> >
>> > > Again, please share the exact log files / description of inputs. What
>> > > does "bad performance" mean?
>> > > --
>> > > Szilárd
>> > >
>> > >
>> > > On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi 
>> > wrote:
>> > > > Dear users,
>> > > >
>> > > > I have two questions.
>> > > >
>> > > >
>> > > > 1. I used to run typical simulations with the following command.
>> > > >
>> > > > gmx mdrun -deffnm md
>> > > >
>> > > > I had no problem.
>> > > >
>> > > >
>> > > > Now I am running a simulation with "Dry_Martini" FF with the
>> following
>> > > > input.
>> > > >
>> > > >
>> > > > integrator   = sd
>> > > > tinit= 0.0
>> > > > dt   = 0.040
>> > > > nsteps   = 100
>> > > >
>> > > > nstlog   = 5000
>> > > > nstenergy= 5000
>> > > > nstxout-compressed   = 5000
>> > > > compressed-x-precision   = 100
>> > > >
>> > > > cutoff-scheme= Verlet
>> > > > nstlist  = 10
>> > > > ns_type  = grid
>> > > > pbc  = xyz
>> > > > verlet-buffer-tolerance  = 0.005
>> > > >
>> > > > epsilon_r= 15
>> > > > coulombtype  = reaction-field
>> > > > rcoulomb = 1.1
>> > > > vdw_type = cutoff
>> > > > vdw-modifier = Potential-shift-verlet
>> > > > rvdw = 1.1
>> > > >
>> > > > tc-grps  = system
>> > > > tau_t= 4.0
>> > > > ref_t= 310
>> > > >
>> > > > ; Pressure coupling:
>> > > > Pcoupl   = no
>> > > >
>> > > > ; GENERATE VELOCITIES FOR STARTUP RUN:
>> > > > gen_vel  = yes
>> > > > gen_temp = 310
>> > > > gen_seed = 1521731368
>> > > >
>> > > >
>> > > >
>> > > > If I use the same command to submit the job.
>> > > > I got the following error. I don't know why.
>> > > >
>> > > > ---
>> > > > Program: gmx mdrun, version 2018.1
>> > > > Source file: src/gromacs/taskassignment/resourcedivision.cpp (line
>> 224)
>> > > >
>> > > > Fatal error:
>> > > > When using GPUs, setting the number of OpenMP threads without
>> > specifying
>> > > the
>> > > > number of ranks can lead to conflicting demands. Please specify the
>> > > number
>> > > > of
>> > > > thread-MPI ranks as well (option -ntmpi).
>> > > >
>> > > > For more information and tips for troubleshooting, please check the
>> > > GROMACS
>> > > > website at http://www.gromacs.org/Documentation/Errors
>> > > > ---
>> > > >
>> > > >
>> > > > So I did run simulation with the following command.
>> > > >
>> > > >
>> > > > gmx mdrun -deffnm md -ntmpi 1
>> > > >
>> > > >
>> > > > Now the performance is extremely bad.
>> > > > Since yesterday, the log file still reporting the first step's
>> energy.
>> > > >
>> > > > 2. This is the second question. Why?
>> > > >
>> > > > Can anyone help?
>> > > >
>> > > >
>> > > > Myunggi Yi
>> > > > --
>> > > > 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
>> > >
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>> > > /Mailing_Lists/GMX-Users_List before posting!
>> > >
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>> > > send a mail to gmx-users-requ...@gromacs.org.
>> > --
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>> >
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>> > posting!
>

[gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)

[Marc Hoemberger]

HI Gromacs users,

I am trying to count water molecules within 1.5nm of a selection residues.
Now I know that for a general counting of all water atoms within a radius
of a set of atoms I can use trjorder, however what I would like to do is to
have *only water molecules that satisfy the distance condition for all the
atoms in my selection*.

Is there a way to do such an analysis that I just did not see in the
manual, or do I have to use other programs to achieve such a goal?

Thanks in advance,
Best
Marc
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Re: [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)

[Mark Abraham]

Hi,

This is what the dynamic selections are for, e.g. as implemented in gmx
select (and some analysis tools).

Mark

On Thu, Mar 29, 2018 at 2:17 PM Marc Hoemberger 
wrote:

> HI Gromacs users,
>
> I am trying to count water molecules within 1.5nm of a selection residues.
> Now I know that for a general counting of all water atoms within a radius
> of a set of atoms I can use trjorder, however what I would like to do is to
> have *only water molecules that satisfy the distance condition for all the
> atoms in my selection*.
>
> Is there a way to do such an analysis that I just did not see in the
> manual, or do I have to use other programs to achieve such a goal?
>
> Thanks in advance,
> Best
> Marc
> --
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Re: [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)

[Marc Hoemberger]

Thanks for your quick response, I was not aware of this and will have a
look at gmx select!

-Marc

On Thu, Mar 29, 2018 at 8:17 AM, Mark Abraham 
wrote:

> Hi,
>
> This is what the dynamic selections are for, e.g. as implemented in gmx
> select (and some analysis tools).
>
> Mark
>
> On Thu, Mar 29, 2018 at 2:17 PM Marc Hoemberger 
> wrote:
>
> > HI Gromacs users,
> >
> > I am trying to count water molecules within 1.5nm of a selection
> residues.
> > Now I know that for a general counting of all water atoms within a radius
> > of a set of atoms I can use trjorder, however what I would like to do is
> to
> > have *only water molecules that satisfy the distance condition for all
> the
> > atoms in my selection*.
> >
> > Is there a way to do such an analysis that I just did not see in the
> > manual, or do I have to use other programs to achieve such a goal?
> >
> > Thanks in advance,
> > Best
> > Marc
> > --
> > 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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> > 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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>



-- 
Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453
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Re: [gmx-users] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??

[Mark Abraham]

Hi,

Note that from 4.6 and until 5.1.x, both the Verlet scheme (which requires
rlist >= cutoff) and the twin-range group scheme (which requires cutoff >=
rlist) were implemented, so the documentation was incomplete. Before
GROMACS 2016, the twin-range scheme was removed and the documentation
corrected.

Mark

On Mon, Mar 26, 2018 at 3:27 PM Szilárd Páll  wrote:

> rlist >= rcoulomb / rvdw is the correct one, the list cutoff has to be
> at least as long as the longest of the interaction cut-offs.
> --
> Szilárd
>
>
> On Mon, Mar 26, 2018 at 1:05 PM, huolei peng 
> wrote:
> > In the user guide of Gromacs 2016 (or 2018), it shows " rlist>=rcoulomb "
> >  or "rlist>=rvdw" in several places (see the links below), which are in
> > contrast to those in version of 5.15.  Are those changes due to typos?
> > Thanks.
> >
> >
> >
> http://manual.gromacs.org/documentation/2016-current/user-guide/mdp-options.html
> >
> >
> http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html
> >
> >
> http://manual.gromacs.org/documentation/5.1-current/user-guide/mdp-options.html
> >
> >
> >
> > Best,
> >
> > Peng
> > --
> > Gromacs Users mailing list
> >
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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] Performance

[Myunggi Yi]

Thanks.

I used the exactly same program (same installation and same environment
variable).

How come this error depends on the *.mdp file?

I don't get it with typical simulations such as md with PME etc,
but I get it with this Dry_Martini mdp file (using sd, reaction field etc.).



Myunggi Yi

On Thu, Mar 29, 2018 at 7:58 AM, Szilárd Páll 
wrote:

> Thanks. Looks like the messages and error handling is somewhat
> confusing; you must have the OMP_NUM_THREADS environment variable set
> which (just as setting -ntomp), without setting -ntmpi too is not
> supported.
>
> Either let mdrun decide about the thread count or set -ntmpi manually.
>
> --
> Szilárd
>
>
> On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi  wrote:
> > Does it work?
> >
> > https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl
> >
> > How about this?
> >
> >
> > Myunggi Yi
> >
> > On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham  >
> > wrote:
> >
> >> Hi,
> >>
> >> Attachments can't be accepted on the list - please upload to a file
> sharing
> >> service and share links to those.
> >>
> >> Mark
> >>
> >> On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi 
> wrote:
> >>
> >> > I am attaching the file.
> >> >
> >> > Thank you.
> >> >
> >> > Myunggi Yi
> >> >
> >> > On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll <
> pall.szil...@gmail.com>
> >> > wrote:
> >> >
> >> > > Again, please share the exact log files / description of inputs.
> What
> >> > > does "bad performance" mean?
> >> > > --
> >> > > Szilárd
> >> > >
> >> > >
> >> > > On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi 
> >> > wrote:
> >> > > > Dear users,
> >> > > >
> >> > > > I have two questions.
> >> > > >
> >> > > >
> >> > > > 1. I used to run typical simulations with the following command.
> >> > > >
> >> > > > gmx mdrun -deffnm md
> >> > > >
> >> > > > I had no problem.
> >> > > >
> >> > > >
> >> > > > Now I am running a simulation with "Dry_Martini" FF with the
> >> following
> >> > > > input.
> >> > > >
> >> > > >
> >> > > > integrator   = sd
> >> > > > tinit= 0.0
> >> > > > dt   = 0.040
> >> > > > nsteps   = 100
> >> > > >
> >> > > > nstlog   = 5000
> >> > > > nstenergy= 5000
> >> > > > nstxout-compressed   = 5000
> >> > > > compressed-x-precision   = 100
> >> > > >
> >> > > > cutoff-scheme= Verlet
> >> > > > nstlist  = 10
> >> > > > ns_type  = grid
> >> > > > pbc  = xyz
> >> > > > verlet-buffer-tolerance  = 0.005
> >> > > >
> >> > > > epsilon_r= 15
> >> > > > coulombtype  = reaction-field
> >> > > > rcoulomb = 1.1
> >> > > > vdw_type = cutoff
> >> > > > vdw-modifier = Potential-shift-verlet
> >> > > > rvdw = 1.1
> >> > > >
> >> > > > tc-grps  = system
> >> > > > tau_t= 4.0
> >> > > > ref_t= 310
> >> > > >
> >> > > > ; Pressure coupling:
> >> > > > Pcoupl   = no
> >> > > >
> >> > > > ; GENERATE VELOCITIES FOR STARTUP RUN:
> >> > > > gen_vel  = yes
> >> > > > gen_temp = 310
> >> > > > gen_seed = 1521731368
> >> > > >
> >> > > >
> >> > > >
> >> > > > If I use the same command to submit the job.
> >> > > > I got the following error. I don't know why.
> >> > > >
> >> > > > ---
> >> > > > Program: gmx mdrun, version 2018.1
> >> > > > Source file: src/gromacs/taskassignment/resourcedivision.cpp
> (line
> >> 224)
> >> > > >
> >> > > > Fatal error:
> >> > > > When using GPUs, setting the number of OpenMP threads without
> >> > specifying
> >> > > the
> >> > > > number of ranks can lead to conflicting demands. Please specify
> the
> >> > > number
> >> > > > of
> >> > > > thread-MPI ranks as well (option -ntmpi).
> >> > > >
> >> > > > For more information and tips for troubleshooting, please check
> the
> >> > > GROMACS
> >> > > > website at http://www.gromacs.org/Documentation/Errors
> >> > > > ---
> >> > > >
> >> > > >
> >> > > > So I did run simulation with the following command.
> >> > > >
> >> > > >
> >> > > > gmx mdrun -deffnm md -ntmpi 1
> >> > > >
> >> > > >
> >> > > > Now the performance is extremely bad.
> >> > > > Since yesterday, the log file still reporting the first step's
> >> energy.
> >> > > >
> >> > > > 2. This is the second question. Why?
> >> > > >
> >> > > > Can anyone help?
> >> > > >
> >> > > >
> >> > > > Myunggi Yi
> >> > > > --
> >> > > > 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/

Re: [gmx-users] Performance

[Myunggi Yi]

Dear Szilard,

Can you run this simulation?

Simulation doesn't crush and doesn't generate error message.
It take forever without updating report in log file or other output files.

Is this a bug?



On Thu, Mar 29, 2018 at 7:58 AM, Szilárd Páll 
wrote:

> Thanks. Looks like the messages and error handling is somewhat
> confusing; you must have the OMP_NUM_THREADS environment variable set
> which (just as setting -ntomp), without setting -ntmpi too is not
> supported.
>
> Either let mdrun decide about the thread count or set -ntmpi manually.
>
> --
> Szilárd
>
>
> On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi  wrote:
> > Does it work?
> >
> > https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl
> >
> > How about this?
> >
> >
> > Myunggi Yi
> >
> > On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham  >
> > wrote:
> >
> >> Hi,
> >>
> >> Attachments can't be accepted on the list - please upload to a file
> sharing
> >> service and share links to those.
> >>
> >> Mark
> >>
> >> On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi 
> wrote:
> >>
> >> > I am attaching the file.
> >> >
> >> > Thank you.
> >> >
> >> > Myunggi Yi
> >> >
> >> > On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll <
> pall.szil...@gmail.com>
> >> > wrote:
> >> >
> >> > > Again, please share the exact log files / description of inputs.
> What
> >> > > does "bad performance" mean?
> >> > > --
> >> > > Szilárd
> >> > >
> >> > >
> >> > > On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi 
> >> > wrote:
> >> > > > Dear users,
> >> > > >
> >> > > > I have two questions.
> >> > > >
> >> > > >
> >> > > > 1. I used to run typical simulations with the following command.
> >> > > >
> >> > > > gmx mdrun -deffnm md
> >> > > >
> >> > > > I had no problem.
> >> > > >
> >> > > >
> >> > > > Now I am running a simulation with "Dry_Martini" FF with the
> >> following
> >> > > > input.
> >> > > >
> >> > > >
> >> > > > integrator   = sd
> >> > > > tinit= 0.0
> >> > > > dt   = 0.040
> >> > > > nsteps   = 100
> >> > > >
> >> > > > nstlog   = 5000
> >> > > > nstenergy= 5000
> >> > > > nstxout-compressed   = 5000
> >> > > > compressed-x-precision   = 100
> >> > > >
> >> > > > cutoff-scheme= Verlet
> >> > > > nstlist  = 10
> >> > > > ns_type  = grid
> >> > > > pbc  = xyz
> >> > > > verlet-buffer-tolerance  = 0.005
> >> > > >
> >> > > > epsilon_r= 15
> >> > > > coulombtype  = reaction-field
> >> > > > rcoulomb = 1.1
> >> > > > vdw_type = cutoff
> >> > > > vdw-modifier = Potential-shift-verlet
> >> > > > rvdw = 1.1
> >> > > >
> >> > > > tc-grps  = system
> >> > > > tau_t= 4.0
> >> > > > ref_t= 310
> >> > > >
> >> > > > ; Pressure coupling:
> >> > > > Pcoupl   = no
> >> > > >
> >> > > > ; GENERATE VELOCITIES FOR STARTUP RUN:
> >> > > > gen_vel  = yes
> >> > > > gen_temp = 310
> >> > > > gen_seed = 1521731368
> >> > > >
> >> > > >
> >> > > >
> >> > > > If I use the same command to submit the job.
> >> > > > I got the following error. I don't know why.
> >> > > >
> >> > > > ---
> >> > > > Program: gmx mdrun, version 2018.1
> >> > > > Source file: src/gromacs/taskassignment/resourcedivision.cpp
> (line
> >> 224)
> >> > > >
> >> > > > Fatal error:
> >> > > > When using GPUs, setting the number of OpenMP threads without
> >> > specifying
> >> > > the
> >> > > > number of ranks can lead to conflicting demands. Please specify
> the
> >> > > number
> >> > > > of
> >> > > > thread-MPI ranks as well (option -ntmpi).
> >> > > >
> >> > > > For more information and tips for troubleshooting, please check
> the
> >> > > GROMACS
> >> > > > website at http://www.gromacs.org/Documentation/Errors
> >> > > > ---
> >> > > >
> >> > > >
> >> > > > So I did run simulation with the following command.
> >> > > >
> >> > > >
> >> > > > gmx mdrun -deffnm md -ntmpi 1
> >> > > >
> >> > > >
> >> > > > Now the performance is extremely bad.
> >> > > > Since yesterday, the log file still reporting the first step's
> >> energy.
> >> > > >
> >> > > > 2. This is the second question. Why?
> >> > > >
> >> > > > Can anyone help?
> >> > > >
> >> > > >
> >> > > > Myunggi Yi
> >> > > > --
> >> > > > 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...@gromac

[gmx-users] Generate unit cell

[ali akgün]

Hello,

I have an polymer pdb file, I want to generate crystal unit structure of
the pdb file.  How can I generate unit cell structure of molecular systems ?

Thank you.
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Re: [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)

[Marc Hoemberger]

I have been reading the manual (specifically gmx help selections  & gmx
select) and trying to apply the correct syntax in reading out water
molecules that satisfy a defined distance to all of my residues.
The manual states that boolean statements are evaluated left to right and
as soon as the first expression is true the next expressions are not
considered anymore. I would like to couple multiple boolean conditions
together but from the manual this seems to be not possible (unless I might
be misunderstanding something)

I have tried to use the following command:

gmx select -f TRJ.xtc -s TOP.tpr -n INDEX.ndx *-select 'group "OW_WATER"
and within 1.5 of resid 157 and within 1.5 of resid 50' *-os POS.xvg -oi
INDI.dat -on INDEX.ndx

which results in all water molecules around 1.5nm of each individual
residue, I would like to get this expressions to evaluate from left to
right completely so that I only get all those atoms that are within 1.5 of
all the mentioned residues (∧), i.e. not a shortcircuited version. Is this
at all possible, or should I try using other programs/scripts for such an
endeavor.
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Re: [gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)

[Marc Hoemberger]

Hi Mark,

I have been reading the manual (specifically gmx help selections  & gmx
select) and trying to apply the correct syntax in reading out water
molecules that satisfy a defined distance to all of my residues.
The manual states that boolean statements are evaluated left to right and
as soon as the first expression is true the next expressions are not
considered anymore. I would like to couple multiple boolean conditions
together but from the manual this seems to be not possible (unless I might
be misunderstanding something)

I have tried to use the following command:

gmx select -f TRJ.xtc -s TOP.tpr -n INDEX.ndx *-select 'group "OW_WATER"
and within 1.5 of resid 157 and within 1.5 of resid 50' *-os POS.xvg -oi
INDI.dat -on INDEX.ndx

which results in all water molecules around 1.5nm of each individual
residue, I would like to get this expressions to evaluate from left to
right completely so that I only get all those atoms that are within 1.5 of
all the mentioned residues (∧), i.e. not a shortcircuited version. Is this
at all possible, or should I try using other programs/scripts for such an
endeavor.

(Sorry for sending the email twice, I accidentally answered to my own mail)

On Thu, Mar 29, 2018 at 8:17 AM, Mark Abraham 
wrote:

> Hi,
>
> This is what the dynamic selections are for, e.g. as implemented in gmx
> select (and some analysis tools).
>
> Mark
>
> On Thu, Mar 29, 2018 at 2:17 PM Marc Hoemberger 
> wrote:
>
> > HI Gromacs users,
> >
> > I am trying to count water molecules within 1.5nm of a selection
> residues.
> > Now I know that for a general counting of all water atoms within a radius
> > of a set of atoms I can use trjorder, however what I would like to do is
> to
> > have *only water molecules that satisfy the distance condition for all
> the
> > atoms in my selection*.
> >
> > Is there a way to do such an analysis that I just did not see in the
> > manual, or do I have to use other programs to achieve such a goal?
> >
> > Thanks in advance,
> > Best
> > Marc
> > --
> > 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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>



-- 
Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453
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Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

[Szilárd Páll]

Hi Jochen,

For that particular benchmark I only measured performance with
1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy
to do the runs on all possible core counts with increments of 1, but
that won't tell a whole lot more than what the performance is of a run
using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even
extrapolating from that 2620 to a E5-2630 v4 and expecting to get a
good estimate is tricky (given that the latter has 25% more cores for
the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake
chips which have different performance characteristics.

As Mark notes, there are some mdp option as well as some system
charateristics that will have a strong influence on performance -- if
tens of % is something you consider "strong" (some users are fine to
be within a 2x ballpark :).

What's worth considering is to try to avoid ending up strongly CPU or
GPU bound from start. That may admittedly could be a difficult task
you would run e.g. both biased MD with large pull groups and all-bonds
constraints with Amber FF on large-ish (>100k) systems as well as
vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same
hardware the former will be more prone to be CPU-bound while the
latter will have relatively more GPU-heavy workload.

There are many factors that influence the performance of a run and
therefore giving a the one right answer to your question is not really
possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is
generally sufficient for "typical" protein simulations to run at >=85%
of peak.

Cheers,
--
Szilárd


On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham  wrote:
> Hi,
>
> On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub  wrote:
>
>> Dear Gromacs community, dear Mark,
>>
>> Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4
>> cores does not help when using a GTX 1080Ti and PME on the GPU.
>>
>
> ... for that particular simulation system.
>
>
>> Unfortunately, there were no data points between 4 and 8 CPU cores,
>> hence it was not clear at which #cores the performance actually levels
>> off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon
>> cores does not help, if not having UB potentials, but I don't have a
>> 1080Ti at hand to test for that.
>>
>
> Those data points may not have been run. Szilard might have the data - this
> was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared.
>
>
>> So my questions are:
>>
>> - At which number of E5-26XXv4 cores does the performance for common
>> systems level off with a 1080Ti for your test system (GLIC)?
>>
>> - Does the answer depend strongly on the mdp settings (in particular on
>> the LJ cutoff)?
>>
>
> Longer LJ cutoff (e.g. from different forcefields) will certainly require
> more non-bonded work, so then fewer CPU cores would be needed to do the
> remaining non-offloaded work. However any sweet spot for a particular .tpr
> would be highly dependent on other effects, such as the ratio of solvent
> (which typically has less LJ and simpler update) to solute, or the density
> of dihedral or U-B interactions. And doing pulling or FEP is very different
> again. The sweet spot for the next project will be elsewhere, sadly.
>
> This would help us a lot when choosing the appropriate CPU for a 1080Ti.
>>
>> Many thanks for any suggestions,
>> Jochen
>>
>> --
>> ---
>> Dr. Jochen Hub
>> Computational Molecular Biophysics Group
>> Institute for Microbiology and Genetics
>> Georg-August-University of Göttingen
>> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
>> 
>> .
>> Phone: +49-551-39-14189 <+49%20551%203914189>
>> http://cmb.bio.uni-goettingen.de/
>> ---
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
> --
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Re: [gmx-users] gmx mindist error

[João M . Damas]

 ACEMD is very simplistic in the types of boxes: it only works with cubbic
boxes.

João

On Tue, Mar 27, 2018 at 10:55 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Yes, I understand what you and Justin refer to. Until your first email I
> completely forgot to consider that certain simulations require variations
> to the normal 3D periodicity, and thus my ramble about the box vectors. It
> makes perfect sense now.
>
> Also, thank you suggesting the alternative using the PDB, really
> appreciated. It can certainly make things easier in this particular case.
>
> Best regards,
> J
>
> On Tue, Mar 27, 2018 at 9:48 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Looking at the code, if your PDB file had suitable CRYST1 fields then you
> > would not have needed a .tpr. I improved the docs a bit at
> > https://gerrit.gromacs.org/#/c/7729/
> >
> > Mark
> >
> > On Tue, Mar 27, 2018 at 8:58 PM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > I have no idea how ACEMD works, but one can certainly imagine an MD
> > > package that hard codes the assumption of a cubic box with normal 3D
> > > periodicity. But there's nothing intrinsic to the file format that
> > implies
> > > any periodicity to a box. That's either a convention, or given by other
> > > information from the user.
> > >
> > > Mark
> > >
> > > On Tue, Mar 27, 2018, 18:26 João Henriques <
> joao.m.a.henriq...@gmail.com
> > >
> > > wrote:
> > >
> > >> I see, I didn't consider that. I was strictly thinking about the
> > geometry
> > >> of the box.
> > >>
> > >> Anyway, with some tricks I managed to build a tpr and am now able to
> > >> calculate the mindist to the periodic image.
> > >>
> > >> Thanks!
> > >> J
> > >>
> > >> On 18:19, Tue, Mar 27, 2018 Mark Abraham 
> > >> wrote:
> > >>
> > >> > Hi,
> > >> >
> > >> > The box sizes say nothing about whether the boundary is fully or
> > >> partially
> > >> > periodic, or screw, or not.
> > >> >
> > >> > Mark
> > >> >
> > >> > On Tue, Mar 27, 2018, 16:13 João Henriques <
> > >> joao.m.a.henriq...@gmail.com>
> > >> > wrote:
> > >> >
> > >> > > Thanks Justin, I was really trying to avoid making a tpr file,
> > >> because my
> > >> > > ACEMD uses the Amber format. I sort of hoped gmx mindist could
> > figure
> > >> it
> > >> > > out from the box components present in the xtc file. In principle,
> > >> > couldn't
> > >> > > it be done by using that info alone? Just curious.
> > >> > >
> > >> > > J
> > >> > >
> > >> > > On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul 
> > >> wrote:
> > >> > >
> > >> > > >
> > >> > > >
> > >> > > > On 3/27/18 9:59 AM, João Henriques wrote:
> > >> > > >
> > >> > > >> Dear users and developers,
> > >> > > >>
> > >> > > >> I am trying to use gmx mindist to calculate the minimum
> distance
> > >> > between
> > >> > > >> periodic images but I get the following error:
> > >> > > >>
> > >> > > >> Fatal error:
> > >> > > >> pbc = no is not supported by g_mindist
> > >> > > >>
> > >> > > >> This is the command I am running:
> > >> > > >>
> > >> > > >> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc
> > >> > > >>
> > >> > > >> Now, I have to admit that the .xtc file I'm using is generated
> by
> > >> > ACEMD
> > >> > > >> and
> > >> > > >> not mdrun, but I used gmx dump to check it and everything looks
> > >> sane.
> > >> > > The
> > >> > > >> cuboid box sizes are clearly specified and I don't understand
> > what
> > >> the
> > >> > > >> problem is...
> > >> > > >>
> > >> > > >> box (3x3):
> > >> > > >> box[0]={ 8.16756e+00,  0.0e+00,  0.0e+00}
> > >> > > >> box[1]={ 0.0e+00,  8.25175e+00,  0.0e+00}
> > >> > > >> box[2]={ 0.0e+00,  0.0e+00,  9.73586e+00}
> > >> > > >>
> > >> > > >> Is gmx mindist reading the box vector lengths from the
> structure
> > >> file
> > >> > > >> instead?
> > >> > > >>
> > >> > > >
> > >> > > > When you don't provide a .tpr file, the program does not know
> what
> > >> type
> > >> > > of
> > >> > > > periodicity the simulation used, so it cannot do the requested
> > >> > > calculation
> > >> > > > because the shifts cannot be calculated.
> > >> > > >
> > >> > > > -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!
> > >> > > >
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> > >> > > >
> > >> >