[gmx-users] Error in ions.tpr generation

[Neha Tiwari]

Dear gmx experts,
The ligand molecule was refined and optimized using G03 calculation and
.itp was generated using the ATB server. Still, I am getting the
following error, dirctly copied from the terminal.
And I am unable to generate any extension files in GROMACS using this .itp.



$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

  :-) GROMACS - gmx grompp, 2018.1 (-:



GROMACS is written by:

 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
Berendsen

Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra

  Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru

 Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus


  Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl

  Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola

Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov

   Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen

 Christian WennbergMaarten 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 grompp, version 2018.1

Executable:   /usr/bin/gmx

Data prefix:  /usr

Working dir:  /home/ya/Desktop/Neha/fecA/gromos

Command line:

  gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



NOTE 1 [file ions.mdp]:

  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

  that with the Verlet scheme, nstlist has no effect on the accuracy of

  your simulation.



Setting the LD random seed to 49113858

Generated 165 of the 1596 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein'

Excluding 3 bonded neighbours molecule type '4JCP'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 2 [file topol.top, line 45350]:

  System has non-zero total charge: -14.00

  Total charge should normally be an integer. See

  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

  for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet



ERROR 1 [file topol.top, line 45350]:

  atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 2 [file topol.top, line 45350]:

  atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 3 [file topol.top, line 45350]:

  atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 4 [file topol.top, line 45350]:

  atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 5 [file topol.top, line 45350]:

  atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 6 [file topol.top, line 45350]:

  atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 7 [file topol.top, line 45350]:

  atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 8 [file topol.top, line 45350]:

  atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 9 [file topol.top, line 45350]:

  atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 10 [file topol.top, line 45350]:

  atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 11 [file topol.top, line 45350]:

  atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 12 [file topol.top, line 45350]:

  atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 13 [file topol.top, line 45350]:

  atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 14 [file topol.top, line 45350]:

  atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 15 [file topol.top, line 45350]:

  atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







There were 2 notes



---

Program: gmx grompp, version 2018.1

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137)



Fatal error:

There were 15 errors in input file(s)



For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---



Please help.
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[gmx-users] regarding calculation on shear viscosity

[shakuntala dhurua]

-- Forwarded message -
From: Madhurima Jana 
Date: Thu, Feb 27, 2020 at 12:10 PM
Subject: Re: problem regarding calculation on shear_viscosity
To: shakuntala dhurua 



Dear All,

I have calculated shear viscosity (from 5 ns production trajectory) of bulk
> water (900 water molecules) by using the following command.
>


> gmx tcaf -n index.ndx -s water_packmol_30a_pro5.tpr  -f
> water_packmol_30a_pro5.trr  -oc water_packmol_30a_pro5_wat_tcaf.xvg ,
>


> In the output file named visc_k.xvg , I found that while the eta values
> for different k are in the range of 0.3 to 0.5 cp,  sudden increase in eta
> value of 12 cp occurs in one case. I am unable to trace the reason behind
> it. Hence I request your help to know if I am doing anything wrong. The
> visc_k.xvg file is attached for your reference.
>

Thanks in advance,
Shakuntala
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[gmx-users] Proximal RDF of water around protein?

[Rajeswari A.]

Hi all,
Is it possible to calculate proximal RDF of water around protein using
gromacs? If not what other programs can I use? Please suggest me.

Thanks,
Rajeswari
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[gmx-users] regressiontests/complex (Failed)

[Navneet Kumar]

-How to solve this problem while installing GROMACS-2018.8 on Dell Tesla
C2050.
-Previously I installed GROMACS-2018.4 had same problem (one test
regressiontests/complex failed) still installed. How does this effect
simulation? What kind of error we get if we use gromacs even after failing
this test and do some kind of simulations.











35/39 Test #35: regressiontests/complex ..***Failed   49.02 sec
  :-) GROMACS - gmx mdrun, 2018.8 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
Berendsen
Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra
  Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
 Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus

  Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl
  Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov
   Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen
 Christian WennbergMaarten 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 2018.8
Executable:   /home/navneet/Downloads/gromacs-2018.8/build/bin/gmx
Data prefix:  /home/navneet/Downloads/gromacs-2018.8 (source tree)
Working dir:  /home/navneet/Downloads/regressiontests-2018.8
Command line:
  gmx mdrun -h


Thanx for Using GROMACS - Have a Nice Day


Abnormal return value for ' gmx mdrun -ntmpi 12  -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Re-running nbnxn-vdw-potential-switch using CPU-based PME
Re-running nbnxn_pme using CPU-based PME

Abnormal return value for ' gmx mdrun -ntmpi 6  -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Re-running octahedron using CPU-based PME
Re-running orientation-restraints using CPU-based PME
Re-running pull_geometry_angle using CPU-based PME
Re-running pull_geometry_angle-axis using CPU-based PME
Re-running pull_geometry_dihedral using CPU-based PME
Re-running swap_x using CPU-based PME
FAILED. Check checkforce.out (2 errors) file(s) in swap_y for swap_y
Re-running swap_y using CPU-based PME
FAILED. Check checkforce.out (1 errors) file(s) in swap_z for swap_z
Re-running swap_z using CPU-based PME
FAILED. Check checkforce.out (1 errors) file(s) in tip4p_continue for
tip4p_continue
3 out of 61 complex tests FAILED

  Start 36: regressiontests/kernel
36/39 Test #36: regressiontests/kernel ...   Passed   81.99 sec
  Start 37: regressiontests/freeenergy
37/39 Test #37: regressiontests/freeenergy ...   Passed   11.30 sec
  Start 38: regressiontests/pdb2gmx
38/39 Test #38: regressiontests/pdb2gmx ..   Passed   16.82 sec
  Start 39: regressiontests/rotation
39/39 Test #39: regressiontests/rotation .   Passed5.86 sec

97% tests passed, 1 tests failed out of 39

Label Time Summary:
GTest  =  15.68 sec (33 tests)
IntegrationTest=   8.81 sec (3 tests)
MpiTest=   0.18 sec (3 tests)
UnitTest   =   6.87 sec (30 tests)

Total Test time (real) = 187.17 sec

The following tests FAILED:
35 - regressiontests/complex (Failed)
Errors while running CTest
CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failed
make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
CMakeFiles/Makefile2:1160: recipe for target
'CMakeFiles/run-ctest-nophys.dir/all' failed
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule'
failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:546: recipe for target 'check' failed
make: *** [check] Error 2

_

Regards
Navneet Kumar
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Re: [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

[Justin Lemkul]

On 2/26/20 8:10 PM, Anh Mai wrote:

Hi all,
Could someone please help me?

I have a question about the *temperature outputs *from the two
packages "gmx traj"
and "gmx energy."

I used the two packages to export the Temperature of a "Protein" group.
Here is what I did.

1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot
Temperature_traj.xvg
gmx analyze -f Temperature_traj.xvg
*Found: Temperature_traj = 250.475 K*
2. gmx energy -f energy.edr
Select "14 Temperature".
*Found: Temperature_energy = 300.137 K*

Our *parameters.mdp* file has:
"...
constraints =  h-bonds
constraint_algorithm = Lincs

tc-grps=  System ; sd integrator (!)
tau_t   =  2.0 ; sd integrator (!)
ref_t   =  300

gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
..."

I don't know why the two temperatures are that much different from each
other, such as by 50 degrees.
Looking forward to an explanation.


gmx traj knows nothing about constraints so the number of degrees of 
freedom for the calculation are incorrect.


-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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[gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

[Anh Mai]

Hi all,
Could someone please help me?

I have a question about the *temperature outputs *from the two
packages "gmx traj"
and "gmx energy."

I used the two packages to export the Temperature of a "Protein" group.
Here is what I did.

   1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot
   Temperature_traj.xvg
   gmx analyze -f Temperature_traj.xvg
   *Found: Temperature_traj = 250.475 K*
   2. gmx energy -f energy.edr
   Select "14 Temperature".
   *Found: Temperature_energy = 300.137 K*

Our *parameters.mdp* file has:
"...
constraints =  h-bonds
constraint_algorithm = Lincs

tc-grps=  System ; sd integrator (!)
tau_t   =  2.0 ; sd integrator (!)
ref_t   =  300

gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
..."

I don't know why the two temperatures are that much different from each
other, such as by 50 degrees.
Looking forward to an explanation.
Thanks a lot.

Sincerely yours,
Anh Mai
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Re: [gmx-users] Umbrella sampling of peptide-membrane system

[Mijiddorj B]

Dear John,

Thank you very much for your advice.

Best regards,
Mijiddorj

Hi,
>
> Justin's tutorial is not a fully generalized procedure for umbrella
> sampling; it shows a workflow for one specific example which is not always
> applicable to other systems.
>
> In general, you don't have to use position restraints for anything in
> umbrella sampling. Justin uses them to keep the fibril in place for
> specific reasons, as noted in the paper he based the tutorial on.
>
> That said, what are you trying to do? Adding restraints to the bilayer is
> probably a bad idea, seeing as how the motion of the bilayer is an
> important physical behavior.
>
> Are you calculating the PMF for a molecule traversing a lipid bilayer? If
> so, there are many examples in the literature that detail a procedure
> that's probably much more relevant to you.
>
> Best,
>
> John
>
>
>
> > Dear GMX users,
> >
> > I would like to ask about position restraint during the umbrella
> sampling.
> > 1. Is it need to make position restraint of lipid bilayer during the
> > umbrella sampling simulation?
> > 2. The position restraint was used for the B chain of amyloid-beta
> > peptides
> > in prof. Justin's tutorial. Can I run the simulations without position
> > restrain of lipid molecules in the case of lipid bilayer?
> > or
> > 3. Can I use the position restraint for only phosphorus atoms of the
> > headgroups of both leaflets?
> >
> > If you have any experience, please let me advise which one is better for
> > this kind of calculation.
> >
> > Best regards,
> >
> > Mijiddorj
> > --
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> > a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
>
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[gmx-users] Can GROMACS compute heat flux?

[James]

Hi,

I am interested in testing thermal conductivity at the nano-scale. LAMMPS
has a command to control thermal flux:

https://lammps.sandia.gov/doc/fix_heat.html

But, I cannot find an equivalent command in GROMACS. I know that
thermostats can be set in GROMACS, but they do not seem to have a notion of
how much energy is added or removed. Is this possible to do in GROMACS?

Sincerely,
James Ryley
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Re: [gmx-users] Fwd: error during ions.tpr genereation.

[Justin Lemkul]

On 2/26/20 1:26 PM, Neha Tiwari wrote:

Dear all,
I want to know if there is any error in the .itp file of ligand attached


The mailing list does not accept attachments.


here, the ligand molecule was refined and optimized using G03 calculation
and .itp was generated using the ATB server.
As I am unable to generate any extension files in GROMACS using this.



If you are getting a specific error, please quote it directly (copy and 
paste from your terminal) and provide it to us. In the absence of an 
actual error, there's nothing anyone can do to help you.


-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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[gmx-users] Fwd: error during ions.tpr genereation.

[Neha Tiwari]

Dear all,
I want to know if there is any error in the .itp file of ligand attached
here, the ligand molecule was refined and optimized using G03 calculation
and .itp was generated using the ATB server.
As I am unable to generate any extension files in GROMACS using this.


Please help.
Neha.
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Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Szilárd Páll]

Hi,

Can you please check the performance when running on a single GPU 2019 vs
2020 with your inputs?

Also note that you are using some peculiar settings that will have an
adverse effect on performance (like manually set rlist disallowing the dual
pair-list setup, and nstcalcenergy=1).

Cheers,

--
Szilárd


On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer  wrote:

> Hello,
>
> here is a link to the logfiles.
>
> https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020
>
> If necessary, I can also provide some more log or tpr/gro/... files.
>
> Cheers,
> Andreas
>
>
> On 26.02.20 16:09, Paul bauer wrote:
> > Hello,
> >
> > you can't add attachments to the list, please upload the files
> > somewhere to share them.
> > This might be quite important to us, because the performance
> > regression is not expected by us.
> >
> > Cheers
> >
> > Paul
> >
> > On 26/02/2020 15:54, Andreas Baer wrote:
> >> Hello,
> >>
> >> from a set of benchmark tests with large systems using Gromacs
> >> versions 2019.5 and 2020, I obtained some unexpected results:
> >> With the same set of parameters and the 2020 version, I obtain a
> >> performance that is about 2/3 of the 2019.5 version. Interestingly,
> >> according to nvidia-smi, the GPU usage is about 20% higher for the
> >> 2020 version.
> >> Also from the log files it seems, that the 2020 version does the
> >> computations more efficiently, but spends so much more time waiting,
> >> that the overall performance drops.
> >>
> >> Some background info on the benchmarks:
> >> - System contains about 2.1 million atoms.
> >> - Hardware: 2x Intel Xeon Gold 6134 („Skylake“) @3.2 GHz = 16 cores +
> >> SMT; 4x NVIDIA Tesla V100
> >>   (similar results with less significant performance drop (~15%) on a
> >> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 („Ivy
> >> Bridge“) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20])
> >> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find
> >> the optimal set. However the performance drop seems to be persistent
> >> for all such options.
> >>
> >> Two representative log files are attached.
> >> Does anyone have an idea, where this drop comes from, and how to
> >> choose the parameters for the 2020 version to circumvent this?
> >>
> >> Regards,
> >> Andreas
> >>
> >
>
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Re: [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory

[Szilárd Páll]

Hi,

Indeed, there is an issue with the GPU detection code's consistency checks
that trip and abort the run if any of the detected GPUs behaves in
unexpected ways (e.g. runs out of memory during checks).

This should be fixed in an upcoming release, but until then as you have
observed, you can always restrict the set of GPUs exposed to GROMACS using
the CUDA_VISIBLE_DEVICES environment variable.

Cheers,


--
Szilárd


On Sun, Feb 23, 2020 at 7:51 AM bonjour899  wrote:

> I think I've temporarily solved this problem. Only when I use
> CUDA_VISIABLE_DEVICE to block the memory-almost-fully-occupied GPUs, I can
> run GROMACS smoothly (using -gpu_id only is useless). I think there may be
> some bug in GROMACS's GPU usage model in a multi-GPU environment (It seems
> like as long as one of the GPUs is fully occupied, GROMACS cannot submit to
> any GPUs and return an error with "cudaFuncGetAttributes failed: out of
> memory").
>
>
>
> Best regards,
> W
>
>
>
>
>  Forwarding messages 
> From: "bonjour899" 
> Date: 2020-02-23 11:32:53
> To:  gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] cudaFuncGetAttributes failed: out of memory
> I also tried to restricting to different GPU using -gpu_id, but still with
> the same error. I've also posting my question on
> https://devtalk.nvidia.com/default/topic/1072038/cuda-programming-and-performance/cudafuncgetattributes-failed-out-of-memory/
> Following is the output of nvidia-smi:
>
>
> +-+
>
> | NVIDIA-SMI 440.33.01 Driver Version: 440.33.01 CUDA Version: 10.2 |
>
>
> |---+--+--+
>
> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
>
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
>
>
> |===+==+==|
>
> | 0 Tesla P100-PCIE... On | :04:00.0 Off | 0 |
>
> | N/A 35C P0 34W / 250W | 16008MiB / 16280MiB | 0% Default |
>
>
> +---+--+--+
>
> | 1 Tesla P100-PCIE... On | :06:00.0 Off | 0 |
>
> | N/A 35C P0 28W / 250W | 10MiB / 16280MiB | 0% Default |
>
>
> +---+--+--+
>
> | 2 Tesla P100-PCIE... On | :07:00.0 Off | 0 |
>
> | N/A 35C P0 33W / 250W | 16063MiB / 16280MiB | 0% Default |
>
>
> +---+--+--+
>
> | 3 Tesla P100-PCIE... On | :08:00.0 Off | 0 |
>
> | N/A 36C P0 29W / 250W | 10MiB / 16280MiB | 0% Default |
>
>
> +---+--+--+
>
> | 4 Quadro P4000 On | :0B:00.0 Off | N/A |
>
> | 46% 27C P8 8W / 105W | 12MiB / 8119MiB | 0% Default |
>
>
> +---+--+--+
>
>
>
>
> +-+
>
> | Processes: GPU Memory |
>
> | GPU PID Type Process name Usage |
>
>
> |=|
>
> | 0 20497 C /usr/bin/python3 5861MiB |
>
> | 0 24503 C /usr/bin/python3 10137MiB |
>
> | 2 23162 C /home/appuser/Miniconda3/bin/python 16049MiB |
>
>
> +-+
>
>
>
>
>
>
>
>  Forwarding messages 
> From: "bonjour899" 
> Date: 2020-02-20 10:30:36
> To: "gromacs.org_gmx-users@maillist.sys.kth.se" <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: cudaFuncGetAttributes failed: out of memory
>
> Hello,
>
>
> I have encountered a weird problem. I've been using GROMACS with GPU on a
> server and always performance good. However when I just reran a job today
> and suddenly got this error:
>
>
>
> Command line:
>
> gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3
>
> Back Off! I just backed up pull.log to ./#pull.log.1#
>
> ---
>
> Program: gmx mdrun, version 2019.4
>
> Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100)
>
>
>
> Fatal error:
>
> cudaFuncGetAttributes failed: out of memory
>
>
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
>
>
> It seems the GPU is 0 occupied and I can run other apps with GPU, but I
> cannot run GROMACS mdrun anymore, even if doing energy minimization.
>
>
>
>
>
>
>
>
>
>
>
>
> --
> 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
> 

Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Andreas Baer]

Hello,

here is a link to the logfiles.
https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020

If necessary, I can also provide some more log or tpr/gro/... files.

Cheers,
Andreas


On 26.02.20 16:09, Paul bauer wrote:

Hello,

you can't add attachments to the list, please upload the files 
somewhere to share them.
This might be quite important to us, because the performance 
regression is not expected by us.


Cheers

Paul

On 26/02/2020 15:54, Andreas Baer wrote:

Hello,

from a set of benchmark tests with large systems using Gromacs 
versions 2019.5 and 2020, I obtained some unexpected results:
With the same set of parameters and the 2020 version, I obtain a 
performance that is about 2/3 of the 2019.5 version. Interestingly, 
according to nvidia-smi, the GPU usage is about 20% higher for the 
2020 version.
Also from the log files it seems, that the 2020 version does the 
computations more efficiently, but spends so much more time waiting, 
that the overall performance drops.


Some background info on the benchmarks:
- System contains about 2.1 million atoms.
- Hardware: 2x Intel Xeon Gold 6134 („Skylake“) @3.2 GHz = 16 cores + 
SMT; 4x NVIDIA Tesla V100
  (similar results with less significant performance drop (~15%) on a 
different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 („Ivy 
Bridge“) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20])
- Several options for -ntmpi, -ntomp, -bonded, -pme are used to find 
the optimal set. However the performance drop seems to be persistent 
for all such options.


Two representative log files are attached.
Does anyone have an idea, where this drop comes from, and how to 
choose the parameters for the 2020 version to circumvent this?


Regards,
Andreas





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Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Paul bauer]

Hello,

you can't add attachments to the list, please upload the files somewhere 
to share them.
This might be quite important to us, because the performance regression 
is not expected by us.


Cheers

Paul

On 26/02/2020 15:54, Andreas Baer wrote:

Hello,

from a set of benchmark tests with large systems using Gromacs 
versions 2019.5 and 2020, I obtained some unexpected results:
With the same set of parameters and the 2020 version, I obtain a 
performance that is about 2/3 of the 2019.5 version. Interestingly, 
according to nvidia-smi, the GPU usage is about 20% higher for the 
2020 version.
Also from the log files it seems, that the 2020 version does the 
computations more efficiently, but spends so much more time waiting, 
that the overall performance drops.


Some background info on the benchmarks:
- System contains about 2.1 million atoms.
- Hardware: 2x Intel Xeon Gold 6134 („Skylake“) @3.2 GHz = 16 cores + 
SMT; 4x NVIDIA Tesla V100
  (similar results with less significant performance drop (~15%) on a 
different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 („Ivy 
Bridge“) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20])
- Several options for -ntmpi, -ntomp, -bonded, -pme are used to find 
the optimal set. However the performance drop seems to be persistent 
for all such options.


Two representative log files are attached.
Does anyone have an idea, where this drop comes from, and how to 
choose the parameters for the 2020 version to circumvent this?


Regards,
Andreas



--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Andreas Baer]

Hello,

from a set of benchmark tests with large systems using Gromacs versions 
2019.5 and 2020, I obtained some unexpected results:
With the same set of parameters and the 2020 version, I obtain a 
performance that is about 2/3 of the 2019.5 version. Interestingly, 
according to nvidia-smi, the GPU usage is about 20% higher for the 2020 
version.
Also from the log files it seems, that the 2020 version does the 
computations more efficiently, but spends so much more time waiting, 
that the overall performance drops.


Some background info on the benchmarks:
- System contains about 2.1 million atoms.
- Hardware: 2x Intel Xeon Gold 6134 („Skylake“) @3.2 GHz = 16 cores + 
SMT; 4x NVIDIA Tesla V100
  (similar results with less significant performance drop (~15%) on a 
different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 („Ivy 
Bridge“) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20])
- Several options for -ntmpi, -ntomp, -bonded, -pme are used to find the 
optimal set. However the performance drop seems to be persistent for all 
such options.


Two representative log files are attached.
Does anyone have an idea, where this drop comes from, and how to choose 
the parameters for the 2020 version to circumvent this?


Regards,
Andreas
-- 
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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

Where did you obtain your PDB? Is this a known crystal structure or other 
experimentally derived structure or is it a homology model? Sometimes the 
initial structures have minor artifacts that make energy minimization 
difficult. Perhaps a short-restrained MD simulation (10ps perhaps) with 
10kJ/mol position restraints could remove these artifacts and then you can 
re-minimize and run your normal mode calculation.

-Micholas


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

From: Katrien Clerx 
Sent: Wednesday, February 26, 2020 8:29 AM
To: Smith, Micholas D. ; gmx-us...@gromacs.org 

Subject: [EXTERNAL] RE: [gmx-users] Normal mode analysis


My structure does not contain any ions. Here are the commands that I used:



gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water 
tip3p -ignh



gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5



gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr

gmx_d mdrun -deffnm cg -v



gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr  -maxwarn 
1

gmx_d mdrun -deffnm bfgs -v



gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr





The used mdp files:

cg.mdp :

; Parameters describing what to do, when to stop and what to save

integrator = cg; Algorithm (cg= Conjugate Gradient 
minimization)

emtol= 0; Stop minimization when the maximum force < 
10.0 kJ/mol/nm

emstep  = 0.1  ; Energy step size

nsteps   = 50; Maximum number of

(minimization) steps to perform

nstcgsteep = 1000

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions

cutoff-scheme   = verlet

nstlist= 1  ; Frequency to update the 
neighbor list and long range forces

ns_type  = grid ; Method to determine 
neighbor list (simple, grid)

rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)

coulombtype   = PME

coulomb-modifier = Potential-shift

rcoulomb-switch = 1.0  ; Treatment of long range 
electrostatic interactions

rcoulomb  = 1.2  ; Short-range electrostatic cut-off

vdwtype = cutoff

vdw-modifier= force-switch

rvdw-switch = 1.0

rvdw  = 1.2; Short-range Van der Waals cut-off

fourierspacing  = 0.12

pme_order   = 4

ewald_rtol  =1e-09

epsilon_surface = 0

pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)





bfgs.mdp:

;mdp for l-bfgs energy minimization

define   = -DFLEXIBLE

constraints  = none

integrator   = l-bfgs





; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions

cutoff-scheme   = verlet

nstlist= 10   ; Frequency to update the 
neighbor list and long range forces

ns_type  = grid ; Method to determine 
neighbor list (simple, grid)

rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)

coulombtype   = Reaction-Field

coulomb-modifier = potential-shift ; Treatment of long range 
electrostatic interactions

rcoulomb-switch = 1.0

rcoulomb  = 1.2  ; Short-range electrostatic cut-off

rvdw =  1.2

vdwtype = Cut-off

vdw-modifier = Force-switch

rvdw_switch = 1.0

fourierspacing  = 0.12

pme_order   = 4

epsilon_surface = 0

ewald_rtol   = 1e-9

pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)





;

; Energy minimizing stuff

;

emtol= 0.0

emstep   = 0.0001

nstcgsteep= 1000

nbfgscorr  = 10

nsteps   = 50





nm.mdp:

;Parameters describing what to do, when to stop and what to save

define   = -DFLEXIBLE

integrator =nm  ;Algorithm(normal mode)



; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions

cutoff-scheme   = verlet

nstlist= 10   ; Frequency to update the 
neighbor list and long range forces

ns_type  = grid ; Method to determine 
neighbor list (simple, grid)

rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)

coulombtype   = Reaction-Field ; Treatment of long 
range electrostatic interactions

coulomb-modifier = potential-shift

rcoulomb-switch = 1.0

rcoulomb  = 1.2  ; Short-range 

Re: [gmx-users] Normal mode analysis

[Katrien Clerx]

My structure does not contain any ions. Here are the commands that I used:

gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water 
tip3p -ignh

gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5

gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr
gmx_d mdrun -deffnm cg -v

gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr  -maxwarn 
1
gmx_d mdrun -deffnm bfgs -v

gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr


The used mdp files:
cg.mdp :
; Parameters describing what to do, when to stop and what to save
integrator = cg; Algorithm (cg= Conjugate Gradient 
minimization)
emtol= 0; Stop minimization when the maximum force < 
10.0 kJ/mol/nm
emstep  = 0.1  ; Energy step size
nsteps   = 50; Maximum number of
(minimization) steps to perform
nstcgsteep = 1000
; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
cutoff-scheme   = verlet
nstlist= 1  ; Frequency to update the 
neighbor list and long range forces
ns_type  = grid ; Method to determine 
neighbor list (simple, grid)
rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)
coulombtype   = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 1.0  ; Treatment of long range 
electrostatic interactions
rcoulomb  = 1.2  ; Short-range electrostatic cut-off
vdwtype = cutoff
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw  = 1.2; Short-range Van der Waals cut-off
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  =1e-09
epsilon_surface = 0
pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)


bfgs.mdp:
;mdp for l-bfgs energy minimization
define   = -DFLEXIBLE
constraints  = none
integrator   = l-bfgs


; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
cutoff-scheme   = verlet
nstlist= 10   ; Frequency to update the 
neighbor list and long range forces
ns_type  = grid ; Method to determine 
neighbor list (simple, grid)
rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)
coulombtype   = Reaction-Field
coulomb-modifier = potential-shift ; Treatment of long range 
electrostatic interactions
rcoulomb-switch = 1.0
rcoulomb  = 1.2  ; Short-range electrostatic cut-off
rvdw =  1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
fourierspacing  = 0.12
pme_order   = 4
epsilon_surface = 0
ewald_rtol   = 1e-9
pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)


;
; Energy minimizing stuff
;
emtol= 0.0
emstep   = 0.0001
nstcgsteep= 1000
nbfgscorr  = 10
nsteps   = 50


nm.mdp:
;Parameters describing what to do, when to stop and what to save
define   = -DFLEXIBLE
integrator =nm  ;Algorithm(normal mode)

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
cutoff-scheme   = verlet
nstlist= 10   ; Frequency to update the 
neighbor list and long range forces
ns_type  = grid ; Method to determine 
neighbor list (simple, grid)
rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)
coulombtype   = Reaction-Field ; Treatment of long 
range electrostatic interactions
coulomb-modifier = potential-shift
rcoulomb-switch = 1.0
rcoulomb  = 1.2  ; Short-range electrostatic cut-off
vdwtype = Cut-off
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw  = 1.2; Short-range Van der Waals cut-off
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  =1e-09
epsilon_surface = 0
pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)

nsteps = 1000



From: Smith, Micholas D.
Sent: woensdag 26 februari 2020 14:10
To: Katrien Clerx; 
gmx-us...@gromacs.org
Subject: Re: [gmx-users] Normal mode analysis

Hmmm

How did you prepare the structure? Also, attachments are stripped from emails 
to the mailing list, can you please provide your mdp file as plain text in your 
reply.



===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge 

Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

Hmmm

How did you prepare the structure? Also, attachments are stripped from emails 
to the mailing list, can you please provide your mdp file as plain text in your 
reply.



===
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 Katrien Clerx 

Sent: Wednesday, February 26, 2020 7:52 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis

Yes I used double precision for everything.



-Katrien







From: Smith, Micholas D.
Sent: woensdag 26 februari 2020 13:39
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Normal mode analysis



Is your build of GROMACS using double precision? NMA typically is performed 
with double precision, which is not the default gromacs build.

-Micholas

===
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 Katrien Clerx 

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] [gmx-users] Normal mode analysis

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using 
Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it 
remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
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Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

Is your build of GROMACS using double precision? NMA typically is performed 
with double precision, which is not the default gromacs build.

-Micholas

===
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 Katrien Clerx 

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] [gmx-users] Normal mode analysis

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using 
Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it 
remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
-- 
Gromacs Users mailing list

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Normal mode analysis

[Katrien Clerx]

Yes I used double precision for everything.



-Katrien







From: Smith, Micholas D.
Sent: woensdag 26 februari 2020 13:39
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Normal mode analysis



Is your build of GROMACS using double precision? NMA typically is performed 
with double precision, which is not the default gromacs build.

-Micholas

===
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 Katrien Clerx 

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] [gmx-users] Normal mode analysis

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using 
Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it 
remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
--
Gromacs Users mailing list

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Re: [gmx-users] Listing residues in gromacs

[Subhomoi Borkotoky]

Hi Christian,

Thank you for your reply. The command worked well. I got the indices of the
residues. I want to calculate the occupancies of the residues near my
reference ion within say 0.5 nm. It will help me a lot if you could suggest
something for it. I have tried gmx distance and gmx mindist with the index
file from gmx select, but not successful.

Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com





On Tue, Feb 18, 2020 at 6:58 PM Christian Blau  wrote:

> Hi Subhomoi,
>
>
> Yes,
>
> gmx select
>
> can do that (see
> http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html)
> 
>
>
> For what you want to do, it's beneficial to have a look at the selection
> syntax here
>
> http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html
> <
> http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html?highlight=selection
> >
>
>
> Best,
>
> Christian
>
> On 2020-02-18 13:14, Subhomoi Borkotoky wrote:
> > Hi,
> >
> > Is there any option in gromacs to list residues/atoms around a reference
> > group? I have checked trjorder , but it only gives number of molecules.
> >
> > Thanks & Regards,
> > --
> > *Subhomoi Borkotoky, Ph. D.*
> > Kusuma School of Biological Sciences,
> > Indian Institute of Technology Delhi,
> > New Delhi-110016,
> > India.
> >
> > Alternate E-mail : subho...@yahoo.com
> >
> > https://scholar.google.co.in/citations?hl=en=1=bJz7GokJ
> --
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> posting!
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[gmx-users] Normal mode analysis

[Katrien Clerx]

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using 
Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it 
remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
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Re: [gmx-users] Thesis developed software; which Open-source License?

[p.c.kroon]

Hi Henry,

Although I'm not a lawyer here's how I understand it. You may want to check it 
with your department/university/company's legal department.

I don't know anything about licensing data, but take a look at creative commons 
licenses if you want it to be open.

See also: https://opensource.org/licenses/
Relicensing (from BSD-3 to something else, for example) can be tedious, 
depending on how many people contributed to your code. Everyone who has a claim 
to the IP (your code) has to agree with the change. If you're the only 
contributor, or if all contributors are nearby, it can be pretty 
straightforward. It's also possible (I think with the same conditions) to have 
different licenses for different users. Either way, users of your code do not 
need to be notified. They can keep using your code under the BSD-3 license 
under which they obtained it.

BSD-3 and MIT are very simple and permissive licenses.
Apache2 is also a very permissive license, but there's a bit more legalese 
involved, reducing ambiguity. This is the license I chose for my FOSS projects 
after consulting with my uni's legal department.
(L)GPL and friends are so-called copy-left licenses. Whenever you use GPL 
licensed code in your project, your code also *must* be GPL licensed. This 
becomes a little fuzzy when you're linking against GPL libraries, or importing 
them in your python code. For this reason LGPL was made, which explicitly 
allows compiling against LGPL licensed libraries without making you also GPL 
license your own code.

As I see it, as long as you haven't looked at GPL licensed source code you can 
license your code however you want. I *think* scripts that just call gmx tools 
do not have to be GPL licensed. I personally consider parameter files to be 
data (and not code subject to the LGPL license). So using/adapting those should 
(I think) be ok.  I don’t know which "original GMX simulated solvated protein 
data" you mean, or how that is licensed.

As I said I know very little about the licensing of data, and I think that in 
general it's something to which not enough attention is being paid (at least up 
until now). Has anyone looked up the license for the RSCB PDB for example?

I hope this helps, and that it's not too factually incorrect 

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Henry Wittler
Sent: Friday, February 21, 2020 10:22 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Thesis developed software; which Open-source License?

Greetings comrades. This question may be somewhat redundant, so dont expect 
reply to every aspect, may ask at RG also. However if anyone have more or less 
insight, please reply.

My thesis has calculation software that are built upon partly innovative and 
partly basic calculation/plotting/graphing software based upon "VMD/tcl” 
coding, GROMACS (GMX) and Python/MatplotlibScipy/Numpy (etc).
The solvated protein data (chap. 6 of thesis) are obtained from GMX 
simulations, moreover the analysis data by VMD/tcl etc.

I have uploaded so far just part of the code (for chap. 4.1) I intend to upload 
code from whole thesis to github link 
https://wittler-github.github.io/A_MD_Analysis_of_Insulin/
The following thesis link(downloadable) contains the calculated data along with 
the graphs.

http://hdl.handle.net/1959.9/568798  (
https://www.researchgate.net/project/A-Molecular-Dynamics-Analysis-of-Insulin)


I mainly want to share the novel GMX simulated data and tools I’ve developed 
from the above-mentioned softwares, that are described in my thesis. I do not 
expect to contribute to GMX directly from this repository, possibly via other 
created repository if so.

Currently I have applied the BSD-3 clause version, which I understand to be the 
most relevant and simple to use. Choice is not set-in stone it appears, however 
if changing I understand one need to notify everyone that has taken part of, or 
are using the code.
The BSD-3 do appears to be one of the most popular for open-source code and 
compatible between different softwares. I thought of using LGPL2 since GMX uses 
that, however BSD-3 does appear more simple to understand. The only innovative 
scripts including GMX are just linux bash/automatic scripts that make the 
simulation of replicas straightforward. Can I share these script under the 
BSD-3 license, even though technically they are modified scripts using standard 
gmx commands (not altering the original gmx software v.5.0.4)? Can I share some 
of the GMX code (parameter files etc) and some of the original GMX simulated 
solvated protein data (in addition to data calculated/graphed by matplotlib 
etc), at my github repository with no issues between BSD-3 license and LGPL2?

The other python, and VMD/tcl softwares I do not see any issue with. Are there 
any clash with these above-mentioned softwares to be aware of?

Any other insights anyone else has here about open-source licensing when 
distributing 

Re: [gmx-users] Umbrella sampling of peptide-membrane system

[John Whittaker]

Hi,

Justin's tutorial is not a fully generalized procedure for umbrella
sampling; it shows a workflow for one specific example which is not always
applicable to other systems.

In general, you don't have to use position restraints for anything in
umbrella sampling. Justin uses them to keep the fibril in place for
specific reasons, as noted in the paper he based the tutorial on.

That said, what are you trying to do? Adding restraints to the bilayer is
probably a bad idea, seeing as how the motion of the bilayer is an
important physical behavior.

Are you calculating the PMF for a molecule traversing a lipid bilayer? If
so, there are many examples in the literature that detail a procedure
that's probably much more relevant to you.

Best,

John



> Dear GMX users,
>
> I would like to ask about position restraint during the umbrella sampling.
> 1. Is it need to make position restraint of lipid bilayer during the
> umbrella sampling simulation?
> 2. The position restraint was used for the B chain of amyloid-beta
> peptides
> in prof. Justin's tutorial. Can I run the simulations without position
> restrain of lipid molecules in the case of lipid bilayer?
> or
> 3. Can I use the position restraint for only phosphorus atoms of the
> headgroups of both leaflets?
>
> If you have any experience, please let me advise which one is better for
> this kind of calculation.
>
> Best regards,
>
> Mijiddorj
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