[gmx-users] trap invalid opcode

[Schulz, Roland]

Hi,

This is usually caused by compiling for a different architecture than you are 
running on. Make sure that the setting for GMX_SIMD is matching what the 
compute node is.

Roland


Date: Mon, 28 Jan 2019 14:22:39 + (UTC)

From: Michael Brunsteiner mailto:mbx0...@yahoo.com>>

To: Gmx Users mailto:gmx-us...@gromacs.org>>

Subject: [gmx-users] trap invalid opcode

Message-ID: 
<1633317768.2254503.1548685359...@mail.yahoo.com>

Content-Type: text/plain; charset=UTF-8



Hi



running a gmx job on a newly set-up debian-buster, with intel i7-3820 CPU, and 
one Nvidia 1060 GTX-6Gb architecture, the job dies without further notice, 
nothing in log file, nor in stdout/stderr ...however in /var/syslogi find 
exactly at the time when gromacs stops this message:



Jan 26 23:42:39 rcpepc00609 kernel: [319870.261302] traps: gmx[21360] trap 
invalid opcode ip:7f68a6ef9ce5 sp:7f68937fddb0 error:0 in 
libgromacs.so.3.5.0[7f68a6418000+13a4000]

this is gmx-2018.5 on `uname -a`

Linux rcpepc00609 4.19.0-1-amd64 #1 SMP Debian 4.19.12-1 (2018-12-22) x86_64 
GNU/Linux gromacs was compiled with:

CC=gcc-7 CXX=g++-7 cmake .. -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on nivida driver 
version is 410.78 and cuda toolkit version is 10.0.130



anybody seen this before or some idea whence this error comes?

thanks!!mic

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[gmx-users] About fprintf and debugging

[Schulz, Roland]

Hi,

You use the debug argument i.e. gmx mdrun -debug 1

Roland


Date: Mon, 28 Jan 2019 14:49:05 + (UTC)

From: Mahmood Naderan mailto:nt_mahm...@yahoo.com>>

To: "gromacs.org_gmx-users"


mailto:gromacs.org_gmx-users@maillist.sys.kth.se>>,
Discussion List for

GROMACS Users 
mailto:gmx-us...@gromacs.org>>

Subject: [gmx-users] About fprintf and debugging

Message-ID: 
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Content-Type: text/plain; charset=UTF-8



Hi

Where should I set the flag in order to see the fprintf statements like ??? 
if (debug) ??? { ??? fprintf(debug, "PME: number of ranks = %d, 
rank = %d\n", ??? cr->nnodes, cr->nodeid);



Any idea?



Regards,

Mahmood

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[gmx-users] How to adjust the default protonation states in martini itp files?

[ZHANG Cheng]

Dear martini friends,


By default, the "martinize.py" will 


1) for backbone atoms, positively charge the N-terminus (atom type Qd), and 
negatively charge the C-terminus (atom type Qa).


2) for side chain chargeable residues, always positively charge the LYS and ARG 
and negatively charge the ASP and GLU.


Now I want to change the protonation states based on a particular pH as 
determined by pdb2pqr server.


1) For backbones, if my N-terminus residue is MET:
1Qd 1   METBB 1  1. ; C
2C5 1   MET   SC1 2  0. ; C



based on "martini_v2.2P_aminoacids.itp" for MET:
;id type resnr residu atom cgnr   charge
 1   P5   1 MET BB 1  0
 2   C5   1 MET SC12  0  



should I change to this?
1P5 1   METBB 1  0. ; C
2C5 1   MET   SC1 2  0. ; C



2) For side chains, e.g. GLU
362P5   165   GLUBB   362  0. ; C
363Qa   165   GLU   SC1   363 -1. ; C



if I do not want GLU to be negatively charged,


based on "martini_v2.2P_aminoacids.itp" for GLU neutral form:
;id type resnr residu atom cgnr   charge
 1   P5 1 GLU0BB 1  0
 2   P1 1 GLU0SC12  0 



should I change to this?
362P5   165   GLU0   BB   362  0. ; C
363P1   165   GLU0  SC1   363  0. ; C



Thank you!


Yours sincerely
Cheng
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Re: [gmx-users] Radius of gyration and moment of inertia

[Dallas Warren]

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123938.html

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sat, 26 Jan 2019 at 05:11, Aishwarya Dhar 
wrote:

> Hi,
> I am trying to find the moment of inertia of an aggregate.
> I have used the command gmx gyrate -f  test.gro -s test.gro -p yes -mol
> yes  -o out.xvg
>
> For two aggregates the the shape is similar but the values are
> very different for Ix Iy Iz
>
> For an aggregate 1
> Ix Iy  Iz
> 81538.8  243689  251837
>
> For aggregate 2
> Ix   Iy Iz
> 144172  498275  517148
> Could you please help me as what could the possible solution?
>
>
>
> Thanks in advance
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Re: [gmx-users] differences in plot between gromacs and vmd

[Dallas Warren]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
https://twitter.com/dr_dbw/status/1066843191159050240
https://twitter.com/dr_dbw/status/909559339366572032

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 28 Jan 2019 at 16:49, Shubhangi Gupta 
wrote:

> Hello,
>
> I have simulated a metalloenzyme, containing zinc, in gromacs for
> 100 ns. When i plot distance between zinc and a specific atom in protein,
> the plots obtained are different in vmd and gromacs (using gmx distance).
> vmd shows that the zinc has moved out of the protein at the end of
> trajectory, whereas gromacs shows it is intact. How can the differences
> between the two be accounted for?
>  The plots are linked here.
>
> https://www.dropbox.com/s/pwrpid0lwnewzet/vmd_image.png?dl=0
> https://www.dropbox.com/s/1v2hzd1g62ldk4y/vmd_plot.png?dl=0
> https://www.dropbox.com/s/b75xdgjlu2urb7y/xmgrace_plot.png?dl=0
>
> Regards,
> Shubhangi Gupta
> PhD Research Scholar (YUS lab)
> Dept of Chemistry
> Indian Institute of Technology Bombay
> Powai, Mumbai-400076.
>
> e-mail ID: ignahbuhs.gup...@gmail.com
>shubhangi_gu...@iitb.ac.in
>
>
> <
> https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=default3&tag=caa22c94-ea74-4abf-a345-c66025e605d8
> >
> I’m
> protected online with Avast Free Antivirus. Get it here — it’s free
> forever.
> <
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> >
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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[gmx-users] delay at start

[Michael Brunsteiner]

Hi,

thanks Szilard for the reply, 
below I include what i get to stdout/stderr and the mdp (log file is
too long) obviously the timings are not accurate due to buffering
but to me it looks as if Gromacs spent reproducibly about 2 minutes
running on ONE thread, and only then switches to use 4. This switch
happens at the time when it starts doing the test runs to establish
the optimal pme grid. these test runs only take a couple of seconds
(about 3000 steps = 6ps of a job which on this architecture does
around 220 ns/d) from then on-wards everything is normal and as expected...

In the log file after job-start it gets quickly to the point
where it says:

"Will do PME sum in reciprocal space for electrostatic interactions."

followed by some lit reference. then is stops there for about 2 minutes
and only then carries on saying:

Using a Gaussian width (1/beta) of 0.384195 nm for Ewald

in these 2 minutes the job runs only on one thread, later it switches to 4.
This is on a work station with Intel i7-3820@3.60GHz + one Nvidia 1060 GTX 6Gb
my gmx is 2018.4 on a recently updated debian testing/buster


===
stderr/stdout: job starts at  01:26:14
===
  :-) GROMACS - gmx mdrun, 2018.4 (-:

    GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. Berendsen
    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen Anton Feenstra  
  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson    Jiri Kraus    
  Carsten Kutzner  Per Larsson  Justin A. Lemkul    Viveca Lindahl  
  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund  Teemu Murtola   
    Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov  
   Michael Shirts Alfons Sijbers Peter Tieleman    Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
   and the project leaders:
    Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, version 2018.4
Executable:   /home/michael/local/gromacs-2018.4-bin-cuda10/bin/gmx
Data prefix:  /home/michael/local/gromacs-2018.4-bin-cuda10
Working dir:  /home/michael/test/test-start-job-delay
Command line:
  gmx mdrun -v -deffnm testd

Reading file testd.tpr, VERSION 2018.4 (single precision)

stops here until about 01:26:32 

Changing nstlist from 50 to 100, rlist from 1.2 to 1.236

Using 1 MPI thread
Using 4 OpenMP threads 

1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  PP:0,PME:0

stops here until 01:28:46 ==

starting mdrun 'system'
100 steps,   2000.0 ps.
^Mstep  200: timed with pme grid 44 48 48, coulomb cutoff 1.200: 332.1 M-cycles
^Mstep  400: timed with pme grid 42 42 44, coulomb cutoff 1.303: 362.5 M-cycles

stops here until 01:28:47 ===

^Mstep  600: timed with pme grid 36 40 40, coulomb cutoff 1.456: 390.1 M-cycles
^Mstep  800: timed with pme grid 40 40 40, coulomb cutoff 1.394: 365.9 M-cycles
^Mstep 1000: timed with pme grid 40 40 42, coulomb cutoff 1.368: 355.7 M-cycles
^Mstep 1200: timed with pme grid 40 42 42, coulomb cutoff 1.328: 343.1 M-cycles
^Mstep 1400: timed with pme grid 40 42 44, coulomb cutoff 1.310: 340.4 M-cycles
^Mstep 1600: timed with pme grid 42 42 44, coulomb cutoff 1.303: 337.4 M-cycles
^Mstep 1800: timed with pme grid 42 44 44, coulomb cutoff 1.268: 325.7 M-cycles
^Mstep 2000: timed with pme grid 42 44 48, coulomb cutoff 1.248: 316.7 M-cycles
^Mstep 2200: timed with pme grid 44 48 48, coulomb cutoff 1.200: 295.9 M-cycles
^Mstep 2400: timed with pme grid 42 44 44, coulomb cutoff 1.268: 324.1 M-cycles
^Mstep 2600: timed with pme grid 42 44 48, coulomb cutoff 1.248: 317.3 M-cycles
^Mstep 2800: timed with pme grid 44 48 48, coulomb cutoff 1.200: 294.8 M-cycles
^M  optimal pme grid 44 48 48, coulomb cutoff 1.200

stops here until 01:28:50 ==



mdp file:

integrator   = md
dt   = 0.002
nsteps   = 100
comm-grps    = System
nstcomm  = 50
;
nstxout  = 25000
nstvout  = 0
nstfout  = 0
nstlog   = 25000
nstenergy 

[gmx-users] About fprintf and debugging

[Mahmood Naderan]

Hi
Where should I set the flag in order to see the fprintf statements like
    if (debug)
    {
    fprintf(debug, "PME: number of ranks = %d, rank = %d\n",
    cr->nnodes, cr->nodeid);

Any idea?

Regards,
Mahmood
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[gmx-users] trap invalid opcode

[Michael Brunsteiner]

Hi 

running a gmx job on a newly set-up debian-buster, with intel i7-3820 CPU, and 
one Nvidia 1060 GTX-6Gb
architecture, the job dies without further notice, nothing in log file, nor in 
stdout/stderr ...however in /var/syslogi find exactly at the time when gromacs 
stops this message:

Jan 26 23:42:39 rcpepc00609 kernel: [319870.261302] traps: gmx[21360] trap 
invalid opcode ip:7f68a6ef9ce5 sp:7f68937fddb0 error:0 in 
libgromacs.so.3.5.0[7f68a6418000+13a4000]
this is gmx-2018.5 on `uname -a`
Linux rcpepc00609 4.19.0-1-amd64 #1 SMP Debian 4.19.12-1 (2018-12-22) x86_64 
GNU/Linux
gromacs was compiled with:
CC=gcc-7 CXX=g++-7 cmake .. -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
nivida driver version is 410.78 and cuda toolkit version is 10.0.130

anybody seen this before or some idea whence this error comes?
thanks!!mic
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Re: [gmx-users] Print Neighbour list

[Paolo Conflitti]

Thank you for your answer.

Unfortunately, that is exactly what I am trying to do. However, what I 
need is more of a custom neighbour search for specific particle-water 
interactions (i.e. one atom against all the neighbour water molecules), 
than a completely new class. And I need to do it at runtime, since I 
will use this information as input for other operations.

However, I think I got the gist of it, thanks to your previous answer.

Again, thanks for everything.

Best,
Paolo

Il 28/01/2019 14:03, Mark Abraham ha scritto:

Hi,

gmx select does this kind of operation already, if what you want to do is
not part of the simulation... It is implemented by its own simple but
fairly efficient search. The neighbor search code is intended for
consumption by the short-range kernels, and you do not want to get involved
with that unless you have to!

Mark

On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti 
wrote:


Thanks for your prompt reply.

I wanted to print the neighbour list to better understand the way it is
processed.
I am currently trying to modify the Gromacs code in order to print only
the neighbour list of the water molecules around a certain atom. I got
inside the code and I found the algorithms that process this kind of
information, but I also wanted to see how the data are organized.
May I ask you if you know of a different way or variable (maybe a
commented line somewhere inside Gromacs) that will allow me to do
something similar?

Best,
Paolo

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Re: [gmx-users] Print Neighbour list

[Mark Abraham]

Hi,

gmx select does this kind of operation already, if what you want to do is
not part of the simulation... It is implemented by its own simple but
fairly efficient search. The neighbor search code is intended for
consumption by the short-range kernels, and you do not want to get involved
with that unless you have to!

Mark

On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti 
wrote:

> Thanks for your prompt reply.
>
> I wanted to print the neighbour list to better understand the way it is
> processed.
> I am currently trying to modify the Gromacs code in order to print only
> the neighbour list of the water molecules around a certain atom. I got
> inside the code and I found the algorithms that process this kind of
> information, but I also wanted to see how the data are organized.
> May I ask you if you know of a different way or variable (maybe a
> commented line somewhere inside Gromacs) that will allow me to do
> something similar?
>
> Best,
> Paolo
>
> --
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Re: [gmx-users] Print Neighbour list

[Paolo Conflitti]

Thanks for your prompt reply.

I wanted to print the neighbour list to better understand the way it is 
processed.
I am currently trying to modify the Gromacs code in order to print only 
the neighbour list of the water molecules around a certain atom. I got 
inside the code and I found the algorithms that process this kind of 
information, but I also wanted to see how the data are organized.
May I ask you if you know of a different way or variable (maybe a 
commented line somewhere inside Gromacs) that will allow me to do 
something similar?


Best,
Paolo

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[gmx-users] g_mmpbsa for rna-rna complex

[Atila Petrosian]

Hi gromacs users,

I want to do md simulation of rna-rna complex. Can I do g_mmpbsa tools for
calculation of Delta G binding?

Best,
Atila
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Re: [gmx-users] Print Neighbour list

[Mark Abraham]

Hi,

That's only supported by the group scheme, which is not the default in
2018.3. Probably the output would only be useful from a single-rank run,
because the searching might be done and reported in terms of indices of
atoms local to the domain being searched, rather than global.

Mark

On Mon, 28 Jan 2019 at 11:50 Paolo Conflitti 
wrote:

> Dear Gromacs community,
>
> I am trying to print the neighbour list of my simulations.
> Following the manual, I added the GMX_DUMP_NL environment variable in my
> .profile bash file (export GMX_DUMP_LN=1). However, I cannot see any
> neighbour list printed in my .log file. I am sure that the env variable
> is properly read, since it appears inside the .log file. I am currently
> using Gromacs 2018.3.
>
> Thank you in advance for any help you may give me.
>
> Best,
> Paolo
>
>
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[gmx-users] Print Neighbour list

[Paolo Conflitti]

Dear Gromacs community,

I am trying to print the neighbour list of my simulations.
Following the manual, I added the GMX_DUMP_NL environment variable in my 
.profile bash file (export GMX_DUMP_LN=1). However, I cannot see any 
neighbour list printed in my .log file. I am sure that the env variable 
is properly read, since it appears inside the .log file. I am currently 
using Gromacs 2018.3.


Thank you in advance for any help you may give me.

Best,
Paolo


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