Re: [gmx-users] can dynamic selection be used with gmx rdf?

[Mark Abraham]

Hi,

One way to check that is to consult the online documentation...
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows
options taking dynamic selections!

Mark

On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E 
wrote:

> Hello all,
> I would like to calculate the rdf between a set of oxygen atoms in a lipid
> bilayer to water. But I would like to include in this calculation only a
> subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I
> wonder if such a dynamic selection is possible combined with the rdf tool.
> Thanks
> Alfredo Cardenas
>
>
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[gmx-users] can dynamic selection be used with gmx rdf?

[Cardenas, Alfredo E]

Hello all,
I would like to calculate the rdf between a set of oxygen atoms in a lipid 
bilayer to water. But I would like to include in this calculation only a subset 
of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I wonder if such 
a dynamic selection is possible combined with the rdf tool.
Thanks
Alfredo Cardenas


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[gmx-users] EuroVis MolVA 2019 Deadline Extension (March 8, 2019)

[Björn Sommer]

*

* MolVA 2019 Deadline Extension (March 8, 2019) ** *


MolVA 2019 - Workshop on Molecular Graphics and Visual Analysis of
Molecular Data co-located with EuroVis 2019 June 3, 2019, Porto, Portugal

*** The submission deadline for full papers as well as short papers has
been extended to March 8, 2019 ***

Suggested topics include, but are not limited to:

- Molecular Graphics

- Visual Analysis of Molecular Data (e.g., molecular structures,
biological networks, and pathways, or omics data)

- Visualization of Dynamic Molecular Data

- Visualization of Large Molecular Systems

- Web-based Molecular Graphics and Visualization

- Immersive Analytics approaches using, e.g., VR/AR technologies

- Tools papers describing new molecular visualization tools or novel
features in existing tools

We invite short papers as well as full papers (2-4 pages for short and
up to 8 pages for full papers, both with an additional page reserved for
references). All papers will undergo a single-stage, double-blind peer
review process. Accepted papers will be published in the EG digital
library. The workshop will be held in Porto, Portugal, June 3, 2019, as
part of EuroVis 2019.

Important Dates (NEW!)



Paper Submission Deadline: March 8, 2019

Notification of Acceptance:April 5, 2019

Camera-ready Deadline:   April 15, 2019

Workshop Date:    June 3, 2019

More info:

http://decibel.fi.muni.cz/~xbyska/molva/

Submission



Please submit your short and full papers via PCS (Deadline: March 8, 2019):

https://new.precisionconference.com/ (EuroVis 2019 MolVA Workshop)  

Please follow the EG guidelines for writing the paper. You can find more
info and templates here:

https://www.eurovis.org/submission-guidelines/

https://www.eurovis.org/files/egPublStyle-EuroVis_full-short-stars-posters-2019.zip

If you have any question, please contact us:

molva.euro...@gmail.com

Best regards,

  Jan Byška, Michael Krone, Björn Sommer

  MolVA 2019 Organizing Committee

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Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS

[Lalehan Ozalp]

Dear Szilárd,

They most certainly are clear! I originally thought the GPU of the terminal
would be very useful. Your suggestions are of great help.
Thank you so much!

Best wishes,
Lalehan
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Re: [gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite

[Kevin Boyd]

Hi,

If it was something fundamentally wrong, you'd see an issue before this.
Martini is just inherently a teensy bit unstable - but this is where the
non-reproducibility of simulations comes in handy; restarting from far
enough away will likely avoid a transiently high energy event.

Kevin

On Tue, Feb 26, 2019 at 4:57 AM zeineb SI CHAIB 
wrote:

> Dear Kevin,
>
> Thank you for your reply.
>
> I did 2 tests:
> 1- I wanted to see in details when the system crashes and which atoms are
> involved so I restarted the simulation from the checkpoint but using a new
> mdp file. The only parameter that I changed was nstxout-compressed  = 1. In
> this case, the simulation didn't crash.
> The command lines that I used were:
> gmx grompp -f md_2.mdp -c npt.gro -p topol.top -n index.ndx -o md_2.tpr
> gmx mdrun -deffnm md_2 -cpi md.cpt -noappend -nt 1
>
> 2- I restarted the simulation from the same checkpoint as in (1), using
> the first mdp file (with nstxout-compressed = 1000) and the simulation
> crashed again at the same step.
> The command line that I used were:
> gmx mdrun -deffnm md -cpi md.cpt -noappend -nt 1
>
> I compared the log files of (1) and (2) and it's starting from the same
> time/steps but as I said (1) didn't crash and (2) crashed.
>
> I can restart the simulation with the new mdp file and keep it running
> again but I want to be sure that It's a random crash and it is not a sign
> of something more fundamentally wrong (physically unrealistic) with my
> system.
>
> Zeineb
>
>
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Re: [gmx-users] Simple way to get last structure from trajectory.

[Mark Abraham]

Hi

OK! I made https://redmine.gromacs.org/issues/2873

Mark

On Wed, 27 Feb 2019 at 00:36 Sergio Perez  wrote:

> Hi,
> Thank you very much for the response. I would like to suggest this
> posibility as a  feature for future editions :)
> Sergio
>
> On Tue, Feb 26, 2019 at 11:36 PM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Unfortunately there is no simple way to get the last frame. Even gmx
> > trjconv -dump doesn't help unless you know quite well what time you seek.
> > So gmx check is your friend.
> >
> > Mark
> >
> > On Tue, 26 Feb 2019 at 08:08 Sergio Perez 
> wrote:
> >
> > > Yes, I understand that, in that case you know how long the simulation
> is.
> > > But what if I don't know how many frames the simulation has  can I
> access
> > > it directly? Or do I need to do a gmx check to see how long the
> > trajectory
> > > is?
> > >
> > > On Tue, Feb 26, 2019 at 12:11 PM aditi singh 
> wrote:
> > >
> > > > You have to dump the last frame: for example*  -1 *for a
> > 1ps/10ns
> > > > trajectory
> > > >
> > > > On Tue, Feb 26, 2019 at 4:31 PM Sergio Perez  >
> > > > wrote:
> > > >
> > > > > Dear gmx comunity,
> > > > >
> > > > > I have tried to get the last structure from a trajectory using:
> > > > >
> > > > > gmx_d trjconv -pbc mol -ur compact -s topol.tpr  -f
> > > > traj_comp.part0001.xtc
> > > > >   -o out.gro -n index.ndx -dump -1
> > > > >
> > > > > But I get the first structure. Maybe the -1 syntax that is used in
> > > python
> > > > > for example does not work here, althought the default value being
> -1
> > > > makes
> > > > > it a little confusing.
> > > > >
> > > > > I am using gmx 2018.1.
> > > > >
> > > > > In addition is there a way to get the last structure without
> knowing
> > > its
> > > > > frame number (like I intended to do). Just to make easier
> > > automatization.
> > > > >
> > > > > Thank you all very much and keep up the good work!
> > > > >
> > > > > Sergio Pérez-Conesa
> > > > > --
> > > > > Gromacs Users mailing list
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> > > > > posting!
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> > > >
> > > >
> > > >
> > > > --
> > > > Aditi
> > > > --
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Re: [gmx-users] WG: Issue with CUDA and gromacs

[Tafelmeier, Stefanie]

Dear Szilárd

I wrote before because of the error message when keeping occurring for mdrun 
simulation:

Assertion failed:
Condition: stat == cudaSuccess
Asynchronous H2D copy failed

As I mentioned all Versions to install (Gormacs, Cuda, nvcc, gcc) are the 
newest once now.

If I run mdrun without further settings it will lead to the error message. If I 
run it and choose the thread amount directly the mdrun is performing well. But 
only for –nt numbers between 1 – 22. Higher ones again lead to the before 
mentioned error message.
 
In order to investigate in more detail, I tried different versions for –nt, 
–ntmpi – ntomp also combined with –npme: 
-   The best performance in the sense of ns/day is with –nt 22 respectively 
–ntomp 22 alone. But then only 22 threads are involved. Which is fine if I run 
more than one mdrun simultaneously, as I can distribute the other 66 threads. 
The GPU usage is then around 65%.
-   A similar good performance is reached with mdrun  -ntmpi 4 -ntomp 18 
-npme 1 -pme gpu -nb gpu. But then 44 threads are involved. The GPU usage is 
then around 50%.

I read the information on 
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html 
which was very helpful, bur some thinsg are not still not clear now to me:
I was wondering if there is any other enhancement of the performance? Or what 
is the reason, that –nt maximum is at 22 threads? Could this be connected to 
the sockets (see details below)? 

Additionally, just I was following the discussion:
I also had the same problem as Lalehan. So I reinstalled with 
-DGMX_OPENMP_MAX_THREADS=128. This changed the error message:

you are using 72 openmp threads, which is larger than GMX_OPENMP_MAX_THREADS 
(64). Decrease the number of OpenMP threads or rebuild GROMACS with a larger 
value for GMX_OPENMP_MAX_THREADS.

To:

Assertion failed:
Condition: stat == cudaSuccess
Asynchronous H2D copy failed


Many thanks for your suggestion before and I would appreciate if you might have 
a hint for these as well.

Best regards,
Steffi



The workstation details are:
Running on 1 node with total 44 cores, 88 logical cores, 1 compatible GPU
Hardware detected:

  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz
Family: 6   Model: 85   Stepping: 4
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov 
cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm 
pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic

Number of AVX-512 FMA units: 2
  Hardware topology: Basic
Sockets, cores, and logical processors:
  Socket  0: [   0  44] [   1  45] [   2  46] [   3  47] [   4  48] [   5  
49] [   6  50] [   7  51] [   8  52] [   9  53] [  10  54] [  11  55] [  12  
56] [  13  57] [  14  58] [  15  59] [  16  60] [  17  61] [  18  62] [  19  
63] [  20  64] [  21  65]
  Socket  1: [  22  66] [  23  67] [  24  68] [  25  69] [  26  70] [  27  
71] [  28  72] [  29  73] [  30  74] [  31  75] [  32  76] [  33  77] [  34  
78] [  35  79] [  36  80] [  37  81] [  38  82] [  39  83] [  40  84] [  41  
85] [  42  86] [  43  87]
  GPU info:
Number of GPUs detected: 1
#0: NVIDIA Quadro P6000, compute cap.: 6.1, ECC:  no, stat: compatible





-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Szilárd Páll
Gesendet: Donnerstag, 31. Januar 2019 17:15
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] WG: Issue with CUDA and gromacs

On Thu, Jan 31, 2019 at 2:14 PM Szilárd Páll  wrote:
>
> On Wed, Jan 30, 2019 at 5:15 PM Tafelmeier, Stefanie
>  wrote:
> >
> > Dear all,
> >
> > We are facing an issue with the CUDA toolkit.
> > We tried several combinations of gromacs versions and CUDA Toolkits. No 
> > Toolkit older than 9.2 was possible to try as there are no driver for 
> > nvidia available for a Quadro P6000.
> > Gromacs
>
> Install the latest 410.xx drivers and it will work; the NVIDIA driver
> download website (https://www.nvidia.com/Download/index.aspx)
> recommends 410.93.
>
> Here's a system with CUDA 10-compatible driver running o a system with
> a P6000: https://termbin.com/ofzo

Sorry, I misread that as "CUDA >=9.2 was not possible".

Note that the driver is backward compatible, so you can use a new
driver with older CUDA versions.

Also note that the oldest driver NVIDIA claims to have P6000 support
is 390.59 which is, as far as I know, one gen older than the 396 that
the CUDA 9.2 toolkit came with. This is however, not something I'd
recommend pursuing, use a new driver from the official site with any
CUDA version that GROMACS supports and it should be fine.

>
> > CUDA
> >
> > Error message
> >
> > 2019
> >
> > 10.0
> >
> > gmx mdrun:
> > Assertion failed:
> > Condition: stat == cudaSuccess
> > Asynchronous H2D copy failed
> >
> > 2019
> >
> > 9.2
> >
> > gmx mdrun:
> > 

Re: [gmx-users] Residue BGC not found in the database

[mary ko]

 Thanks Justin. How should I check if there is a Ter between protein and 
glucose ? If I get you right, for my protein and Bglc system I just need the 
Bgc in the .pdb to be changed to Bglc. Do I need to seprate Bglc from the 
protein and follow the tutorial or can it be regarded as a complex of 
protein-ligand and I can go ahead with pdb2gmx -f .pdb ?  I tried pdb2gmx and 
got this error  :  there were 233 missing atoms in molecule other, if you want 
to use this incomplete topology anyhow use the option -missing. I continued 
with the-missing flag but there built an incomplete topology. In the energy 
minimizationit stops with the  :  'simulation ended prematurely no perrformance 
report will be written'. Should I continue regardless of the incomplete 
topology and this message ? 
On Monday, February 25, 2019, 7:10:35 PM EST, Justin Lemkul 
 wrote:  
 
 

On 2/25/19 4:26 PM, mary ko wrote:
>  Thank you Justin. I am actually following the protein-ligand tutorial to do 
>simulations of my protein-ligand system. I skipped the python 
>cgenff_charmm2gmx.py... Because of the mismatch of cgenff error couldnt be 
>fixed. I have the bgc which is beta-D-glucose and built its .gro file as a 
>ligand and protein-processed.gro and I copied the ligand in the 
>protein-processed.gro to have the complex.gro. I also use charmm36-nov2018 and 
>added it in the force fields with the Bglc to Bgc change in merged.rtp. Now 
>that I try to build the topology.top file with pdb2gmx or even x2top there is 
>an error: atom ot1 in residue Phe was not found in rtp entry Phe with 20 atoms 
>while sorting atoms for pdb2gmx and could only find a force field type for 
>19078 out of 21750 atoms for x2top. What do you think I should do to build the 
>topology?Thanks.

If you have a protein with BGLC as the ligand, use pdb2gmx and make sure 
there is a TER between the protein and glucose, or otherwise a change in 
chain identifier. Do not use x2top and do not modify merged.rtp (modify 
the residue names in the PDB file instead).

-Justin

>      On Saturday, February 23, 2019, 6:50:39 PM EST, Justin Lemkul 
> wrote:
>  
>  
>
> On 2/20/19 11:19 AM, mary ko wrote:
>> Dear all,
>> I face the 'Residue BGC not found in the database' error when I try to build 
>> the topology file of my protein-ligand system by pdb2gmx -f pro.pdb. I used 
>> Charmm force field but I tried it with all the other force fields as well to 
>> see if the problem could be solved which was useless. I searched the list 
>> and errors-gromacs in the website and found that the simplest way is to 
>> change the name of this residue. As I am not familiar with protein 
>> structure, I do not know what changes may be helpful to pass this error. 
>> also, it is said that one way is to parameterize the residue which I do not 
>> know how to do that. Your help would be highly appreciated.Thanks!
> If "BGC" is a synonym for beta-D-glucose, that is called BGLC in CHARMM,
> so you just need to rename the residue accordingly. If it is some other
> unknown species, then yes, you need to parametrize it yourself.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] avoid typing input

[antonia vyrkou]

It does! Thank you

On Wed, 27 Feb 2019, 13:38 Quyen Vu,  wrote:

> hope this help
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> On Wed, Feb 27, 2019 at 2:17 PM antonia vyrkou  wrote:
>
> > hello,
> >
> > is there a way to execute an interactive gromacs command  (for example
> gmx
> > rmsf , choosing a group number from an index file) without typing the
> > number but "reading" it from a file or from a while loop?
> > Does that make sense?
> > --
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Re: [gmx-users] avoid typing input

[antonia vyrkou]

Thank you!

On Wed, 27 Feb 2019, 13:38 Justin Lemkul,  wrote:

>
>
> On 2/27/19 8:16 AM, antonia vyrkou wrote:
> > hello,
> >
> > is there a way to execute an interactive gromacs command  (for example
> gmx
> > rmsf , choosing a group number from an index file) without typing the
> > number but "reading" it from a file or from a while loop?
> > Does that make sense?
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] avoid typing input

[Quyen Vu]

hope this help
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

On Wed, Feb 27, 2019 at 2:17 PM antonia vyrkou  wrote:

> hello,
>
> is there a way to execute an interactive gromacs command  (for example gmx
> rmsf , choosing a group number from an index file) without typing the
> number but "reading" it from a file or from a while loop?
> Does that make sense?
> --
> 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] avoid typing input

[Justin Lemkul]

On 2/27/19 8:16 AM, antonia vyrkou wrote:

hello,

is there a way to execute an interactive gromacs command  (for example gmx
rmsf , choosing a group number from an index file) without typing the
number but "reading" it from a file or from a while loop?
Does that make sense?

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] How to use reduced unit in gromacs?

[Quyen Vu]

Have you checked gromacs manual? for example version of 2019.1 on page 299

On Wed, Feb 27, 2019 at 2:12 PM 이영규  wrote:

> Dear gromacs users,
>
> These days, I am working on supercritical fluid of lennard jones fluid. I
> want to make a system of supercritical fluid by using gromacs with reduced
> units. However, I am lost defining those parameters in gromacs. Could
> anyone help me to figure out this problem?
>
> Thanks in advance.
>
> Best regards
>
> --
>
> Yeongkyu Lee
>
> M.S student
>
> Department of Physics
>
> 501, Jinjudaero, Jinju, Gyeongnam
> <
> https://maps.google.com/?q=501,+Jinjudaero,+Jinju,+Gyeongnam=gmail=g
> >,
> 52828, Korea
>
> Email: monsterpl...@gmail.com
>
> Phone: +82-10-8771-2190
> --
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>
> * Please search the archive at
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Re: [gmx-users] Error detecting AMD GPU in GROMACS 2019.1

[Szilárd Páll]

Michael,

We have the issue pinned down and will be fixed soon. Thanks for the
feedback.

--
Szilárd


On Tue, Feb 26, 2019 at 5:46 AM Michael Williams <
michael.r.c.willi...@gmail.com> wrote:

> Hi Szilárd,
>
> I think these two files (from the complex/nbnxn-ljpme-LB test, just as an
> example) fit under the 50 kB size limit. The only additional notice I see
> (in mdrun.out) is: "WARNING: While sanity checking device #1,
> clBuildProgram did not succeed -11: CL_BUILD_PROGRAM_FAILURE"
>
> I’m not sure if it is relevant, but the AMD GPU is elsewhere identified as
> #0 while the Intel integrated chip is called GPU #1. Thanks again, and
> please let me know if these were not the output files you were looking for.
>
> Mike
>
>
>
> > On Feb 26, 2019, at 1:56 AM, Szilárd Páll 
> wrote:
> >
> > Michael,
> >
> > Can you please post the full stdandard and log outputs (preferably
> through
> > an external service). Having looked at the code, there must be an
> addition
> > output that tells what type of error occurred during the sanity checks
> that
> > produce the result you show.
> >
> > In general, this likely means that the Apple compiler is not happy about
> > the new sanity checks we implemented to improve the robustness of the
> > OpenCL support..
> >
> > --
> > Szilárd
> >
> >
> > On Sun, Feb 24, 2019 at 7:28 AM Michael Williams <
> > michael.r.c.willi...@gmail.com> wrote:
>
> --
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Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS

[Szilárd Páll]

The Quadro K2200 is a low-end several generations old GPU and I strongly
doubt you will see any benefit from using it.

I suggest you try running
mdrun -nb gpu -ntmpi 1 -ntomp 36 -pin on
which will give you the (most likely best) performance you can get when
using both high-end Intel CPUs and the GPU.
Compare that to:
mdrun -nb cpu -ntmpi 1 -ntomp 36 -pin on
mdrun -nb cpu -ntmpi 36 -ntomp 2 -pin on [with or without -npme 0]
mdrun -nb cpu -ntmpi 18 -ntomp 4 -pin on [with or without -npme 0]
I suspect one of the the latter two will be fastest.

You can also try using no domain-decomposition and 72 threads per rank by
recompiling GROMACS and setting the
cmake . -DGMX_OPENMP_MAX_THREADS=128
option. I will could end up being faster than the first suggested CPU run,
but not likely to be faster (by a relevant amount of any) than the latter
two.

If the above technicalities are not clear and you would like to learn about
them to understand them better, I recommend reading (again?) the relevant
parts of the user guide.

Cheers,
--
Szilárd


On Wed, Feb 27, 2019 at 12:27 PM Lalehan Ozalp 
wrote:

> Dear Szilárd,
> There is indeed one GPU. And please keep in mind I used to exploit the -nt
> 72 option BEFORE the 2019-dev version. It looks like it employs GPU by
> default and I don't know how to efficiently use it, apparently.  Here is
> the info you asked for:
> System size: 130655 atoms
>
> .mdp file:
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 1500   ; 2 * 1500 = 3 ps (30 ns)
> dt  = 0.002 ; 2 fs
> ; Output control
> nstenergy   = 5000  ; save energies every 10.0 ps
> nstlog  = 5000  ; update log file every 10.0 ps
> nstxout-compressed  = 5000  ; save coordinates every 10.0 ps
> ; Bond parameters
> continuation= yes   ; continuing from NPT
> constraint_algorithm= lincs ; holonomic constraints
> constraints = h-bonds   ; bonds to H are constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighbor searching and vdW
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 20; largely irrelevant with Verlet
> rlist   = 1.2
> vdwtype = cutoff
> vdw-modifier= force-switch
> rvdw-switch = 1.0
> rvdw= 1.2   ; short-range van der Waals cutoff (in
> nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> rcoulomb= 1.2
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling
> tcoupl  = V-rescale ; modified
> Berendsen thermostat
> tc-grps = Protein_nap_16 Water_and_ions; two coupling
> groups - more accurate
> tau_t   = 0.1   0.1 ; time constant, in
> ps
> ref_t   = 300   300 ; reference
> temperature, one for each group, in K
> ; Pressure coupling
> pcoupl  = Parrinello-Rahman ; pressure coupling
> is on for NPT
> pcoupltype  = isotropic ; uniform scaling
> of box vectors
>
>
>
> my command:
> gmx mdrun -deffnm md_0_30 -ntmpi 4 -ntomp 18 -npme 1 -pme gpu -nb gpu
>
>
>
> and what the program prints in the log file once I run it:
>
> GROMACS version:2019-dev
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:CUDA
> SIMD instructions:  NONE
> FFT library:fftw-3.3.8
> RDTSCP usage:   disabled
> TNG support:enabled
> Hwloc support:  disabled
> Tracing support:disabled
> Built on:   2019-01-22 13:53:24
> Build CPU vendor:   Unknown
> Build CPU brand:Unknown
> Build CPU family:   0   Model: 0   Stepping: 0
> Build CPU features: Unknown
> C compiler: /usr/local/bin/gcc GNU 5.3.0
> C++ compiler flags: -std=c++11  -Wundef -Wextra
> -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations
> -Wall  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
> -Wno-array-bounds
> CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
> Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, V8.0.61
>
> Running on 1 node with total 36 cores, 72 logical cores, 1 compatible GPU
> Hardware detected:
>   CPU info:
> Vendor: Intel
> Brand:  Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz
> Family: 6   Model: 63   Stepping: 2
>
>  GPU info:
> Number of GPUs detected: 1
> #0: NVIDIA 

[gmx-users] avoid typing input

[antonia vyrkou]

hello,

is there a way to execute an interactive gromacs command  (for example gmx
rmsf , choosing a group number from an index file) without typing the
number but "reading" it from a file or from a while loop?
Does that make sense?
-- 
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[gmx-users] How to use reduced unit in gromacs?

[이영규]

Dear gromacs users,

These days, I am working on supercritical fluid of lennard jones fluid. I
want to make a system of supercritical fluid by using gromacs with reduced
units. However, I am lost defining those parameters in gromacs. Could
anyone help me to figure out this problem?

Thanks in advance.

Best regards

-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
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Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS

[Lalehan Ozalp]

Dear Szilárd,
There is indeed one GPU. And please keep in mind I used to exploit the -nt
72 option BEFORE the 2019-dev version. It looks like it employs GPU by
default and I don't know how to efficiently use it, apparently.  Here is
the info you asked for:
System size: 130655 atoms

.mdp file:
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1500   ; 2 * 1500 = 3 ps (30 ns)
dt  = 0.002 ; 2 fs
; Output control
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
nstxout-compressed  = 5000  ; save coordinates every 10.0 ps
; Bond parameters
continuation= yes   ; continuing from NPT
constraint_algorithm= lincs ; holonomic constraints
constraints = h-bonds   ; bonds to H are constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 20; largely irrelevant with Verlet
rlist   = 1.2
vdwtype = cutoff
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw= 1.2   ; short-range van der Waals cutoff (in
nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb= 1.2
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified
Berendsen thermostat
tc-grps = Protein_nap_16 Water_and_ions; two coupling
groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in
ps
ref_t   = 300   300 ; reference
temperature, one for each group, in K
; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling
is on for NPT
pcoupltype  = isotropic ; uniform scaling
of box vectors



my command:
gmx mdrun -deffnm md_0_30 -ntmpi 4 -ntomp 18 -npme 1 -pme gpu -nb gpu



and what the program prints in the log file once I run it:

GROMACS version:2019-dev
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:CUDA
SIMD instructions:  NONE
FFT library:fftw-3.3.8
RDTSCP usage:   disabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2019-01-22 13:53:24
Build CPU vendor:   Unknown
Build CPU brand:Unknown
Build CPU family:   0   Model: 0   Stepping: 0
Build CPU features: Unknown
C compiler: /usr/local/bin/gcc GNU 5.3.0
C++ compiler flags: -std=c++11  -Wundef -Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations
-Wall  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
-Wno-array-bounds
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, V8.0.61

Running on 1 node with total 36 cores, 72 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz
Family: 6   Model: 63   Stepping: 2

 GPU info:
Number of GPUs detected: 1
#0: NVIDIA Quadro K2200, compute cap.: 5.0, ECC:  no, stat: compatible

Highest SIMD level requested by all nodes in run: AVX2_256
SIMD instructions selected at compile time:   None
This program was compiled for different hardware than you are running on,
which could influence performance.
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.



Hardware:

Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):72
On-line CPU(s) list:   0-71
Thread(s) per core:2
Core(s) per socket:18
Socket(s): 2
NUMA node(s):  2
Vendor ID: GenuineIntel
CPU family:6
Model: 63
Model name:Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz
Stepping:  2
CPU MHz:   1200.000
BogoMIPS:  4589.66
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  46080K
NUMA node0 CPU(s): 0-17,36-53
NUMA node1 CPU(s): 18-35,54-71



GPU:

03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL
[Quadro K2200] 

Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS

[Lalehan Ozalp]

Dear Carsten,  thank you for your advice. I'd tried gmx mdrun -deffnm
md_0_30 -ntmpi 4 -ntomp 18 -npme 1 -pme gpu -nb gpu, then tried -ntmpi 8
-ntomp 9, later tried -ntmpi 12 -ntomp 6 (the rest of the command being the
same) and I feel like neither of them make much of a difference. The CPU
performance doesn't seem bad, but the steps are not flowing fast enough. My
system involves 130655 atoms and I'm absolutely sure I ran simulation with
the very same system a month ago, finishing within 2-3 days by only using
option -nt 72. It was the 2016.3 version in which GPU support was disabled.
I'm afraid I don't know how to exploit GPU in the most possible efficient
way.
Anyways, thank you for your suggestion!
Lalehan
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Re: [gmx-users] Simple way to get last structure from trajectory.

[Sergio Perez]

Hi,
Thank you very much for the response. I would like to suggest this
posibility as a  feature for future editions :)
Sergio

On Tue, Feb 26, 2019 at 11:36 PM Mark Abraham 
wrote:

> Hi,
>
> Unfortunately there is no simple way to get the last frame. Even gmx
> trjconv -dump doesn't help unless you know quite well what time you seek.
> So gmx check is your friend.
>
> Mark
>
> On Tue, 26 Feb 2019 at 08:08 Sergio Perez  wrote:
>
> > Yes, I understand that, in that case you know how long the simulation is.
> > But what if I don't know how many frames the simulation has  can I access
> > it directly? Or do I need to do a gmx check to see how long the
> trajectory
> > is?
> >
> > On Tue, Feb 26, 2019 at 12:11 PM aditi singh  wrote:
> >
> > > You have to dump the last frame: for example*  -1 *for a
> 1ps/10ns
> > > trajectory
> > >
> > > On Tue, Feb 26, 2019 at 4:31 PM Sergio Perez 
> > > wrote:
> > >
> > > > Dear gmx comunity,
> > > >
> > > > I have tried to get the last structure from a trajectory using:
> > > >
> > > > gmx_d trjconv -pbc mol -ur compact -s topol.tpr  -f
> > > traj_comp.part0001.xtc
> > > >   -o out.gro -n index.ndx -dump -1
> > > >
> > > > But I get the first structure. Maybe the -1 syntax that is used in
> > python
> > > > for example does not work here, althought the default value being -1
> > > makes
> > > > it a little confusing.
> > > >
> > > > I am using gmx 2018.1.
> > > >
> > > > In addition is there a way to get the last structure without knowing
> > its
> > > > frame number (like I intended to do). Just to make easier
> > automatization.
> > > >
> > > > Thank you all very much and keep up the good work!
> > > >
> > > > Sergio Pérez-Conesa
> > > > --
> > > > 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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