Re: [gmx-users] cpu/gpu utilization

[Mahmood Naderan]

>(try the other parallel modes)

Do you mean OpenMP and MPI?


>- as noted above try offloading only the nonbondeds (or possibly the hybrid 
>PME mode -pmefft cpu)

May I know how? Which part of the documentation says about that?


Regards,
Mahmood

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[gmx-users] An atom is beyond the wall in gromacs2018

[Joel Awuah]

 Hi Gromacs Users
I did a simulated annealing MD with gromacs/5.0.1 and gromacs/2018. In both
cases I had the same input configuration and parameters for the potential
wall. The simulation with gromacs/5.0.1 did achieve convergence but with
the gromacs/2018, an atom always go beyond the wall. Can someone please
help figure out what the problem with the gromacs/2018 one.

Cheers
Joel



-- 
Joel Baffour Awuah
PhD Candidate
*Institute for Frontier Materials*

*Deakin University*
*Waurn Ponds, 3126 VIC*
*Australia +61450070635*
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Re: [gmx-users] cpu/gpu utilization

[Szilárd Páll]

PS:
Care to know what can you do?
- as noted above try offloading only the nonbondeds (or possibly the hybrid
PME mode -pmefft cpu)
- check if your GPU has application clocks that can be bumped
- if you have the means, consider getting a bit faster GPU; the Quadro
M2000 in your machine is both slightly dated and low-end  similar board as
the GTX 950



--
Szilárd

On Wed, Feb 28, 2018 at 10:26 PM, Szilárd Páll 
wrote:

> Thanks!
>
> Looking at the log file, as I guessed earlier, you can see the following:
>
> - Given that you have a rather low-end GPU and a fairly fast workstation
> CPU the run is *very* GPU-bound: the CPU spends 16.4 + 54.2 = 70.6% waiting
> for the GPU (see lines 628 and 630)
>
> - this means that the default behavior of offloading both the nonbonded
> and PME tasks to the GPU is not beneficial (try the other parallel modes)
>
> - mdrun is still using 8 cores / 16 threads *for the parts of the run that
> require it* (Bonded forces (2.7%), Integration / Constraints (2.6 % / 4.9
> %) etc.), but as this takes <30% of the runtime, that gives you your
> average of 4.5 utilization (0.3*16 = 4.8). That you "see" 9 threads active
> is just the averaging/sampling effect of from your minitoring tools.
>
> Cheers,
>
> --
> Szilárd
>
> On Wed, Feb 28, 2018 at 10:12 PM, Mahmood Naderan 
> wrote:
>
>> >The list does not accept attachments, so please use a file sharing or
>> content sharing website so >everyone can see your data and has the context.
>>
>> I uploaded here
>>
>> https://pastebin.com/RCkkFXPx
>>
>>
>>
>> Regards,
>> Mahmood
>>
>>
>
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Re: [gmx-users] cpu/gpu utilization

[Szilárd Páll]

Thanks!

Looking at the log file, as I guessed earlier, you can see the following:

- Given that you have a rather low-end GPU and a fairly fast workstation
CPU the run is *very* GPU-bound: the CPU spends 16.4 + 54.2 = 70.6% waiting
for the GPU (see lines 628 and 630)

- this means that the default behavior of offloading both the nonbonded and
PME tasks to the GPU is not beneficial (try the other parallel modes)

- mdrun is still using 8 cores / 16 threads *for the parts of the run that
require it* (Bonded forces (2.7%), Integration / Constraints (2.6 % / 4.9
%) etc.), but as this takes <30% of the runtime, that gives you your
average of 4.5 utilization (0.3*16 = 4.8). That you "see" 9 threads active
is just the averaging/sampling effect of from your minitoring tools.

Cheers,

--
Szilárd

On Wed, Feb 28, 2018 at 10:12 PM, Mahmood Naderan 
wrote:

> >The list does not accept attachments, so please use a file sharing or
> content sharing website so >everyone can see your data and has the context.
>
> I uploaded here
>
> https://pastebin.com/RCkkFXPx
>
>
>
> Regards,
> Mahmood
>
>
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Re: [gmx-users] cpu/gpu utilization

[Mahmood Naderan]

>The list does not accept attachments, so please use a file sharing or content 
>sharing website so >everyone can see your data and has the context.

I uploaded here

https://pastebin.com/RCkkFXPx



Regards,
Mahmood

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Re: [gmx-users] cpu/gpu utilization

[Szilárd Páll]

The list does not accept attachments, so please use a file sharing or
content sharing website so everyone can see your data and has the context.

--
Szilárd

On Wed, Feb 28, 2018 at 7:51 PM, Mahmood Naderan 
wrote:

> >Additionally, you still have not provided the *mdrun log file* I
> requested. top output is not what I asked for.
> See the attached file.
>
>
> Regards,
> Mahmood
>
>
>
>
>
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[gmx-users] Pressure using solvation shell

[Abramyan, Tigran]

Dear Gromacs Users,


I am using a solvation shell (-shell command) around a large nucleosome system 
to accelerate the simulation speed, and was wondering what ensemble is 
suggested to run such a system in a solvation shell?


After a few trial runs using NPT equilibration with and without constraining 
the solute, I noticed that NPT squeezed the system in a way that in PBC the 
protein is 'touching' itself in the periodic image. I see that the system 
pressure is close to 1 bar at the beginning of NPT at frame 0, Pressure (bar) 
-8.50289. Does this mean NPT can be skipped and all equilibration and 
production run could be run in NVT?


Please advise,


Thanks,

Tigran


--
Tigran M. Abramyan, Ph.D.
Postdoctoral Fellow, Computational Biophysics & Molecular Design
Center for Integrative Chemical Biology and Drug Discovery
Eshelman School of Pharmacy
The University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7363

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 166, Issue 129

[Marc Hoemberger]

Hi Justin,

I did try to reproduce the behavior of the GPU-calculation crash with a
vanilla gromacs (5.1.4) version. No matter if I use vanilla gromacs or the
patched gromacs version I do see that on CPU node only the calculation runs
without problems, as soon as I try to run the simulation with GPU the
simulation crashes with the aforementioned error.

I am currently compiling gromacs 2018 and will report back if I see the
same behavior for gromacs 2018.


-Marc


> Message: 2
> Date: Wed, 28 Feb 2018 13:13:22 -0500
> From: Marc Hoemberger 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Gromacs on CPU runs fine, same calculation
> crashes on GPU with nonbonded interaction larger than table limit
> Message-ID:
> 

Re: [gmx-users] cpu/gpu utilization

[Mahmood Naderan]

>Additionally, you still have not provided the *mdrun log file* I requested. 
>top output is not what I asked for.
See the attached file.


Regards,
Mahmood




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Re: [gmx-users] Backup files

[Mark Abraham]

Hi,

Setting GMX_MAXBACKUP=-1 is as easy as it can get :-)

Mark

On Wed, Feb 28, 2018 at 7:03 PM Mahmood Naderan 
wrote:

> Well I searched for "gromacs backoff" first and then while googling I saw
> [1] and an environment variable GMX_MAXBACKUP [2].
>
>
> [1] http://cupnet.net/clean-gromacs-backups
>
> [2] Environment Variables — GROMACS 5.1 documentation
>
>
> Therefore I asked for a simpler method ;)
> Anyway...
>
>
> Regards,
> Mahmood
>
>
> On Wednesday, February 28, 2018, 8:15:34 PM GMT+3:30, Mark Abraham <
> mark.j.abra...@gmail.com> wrote:
>
>
> There's an even better solution in the GROMACS documentation, which e.g.
> googling "disable gromacs backups" will find ;-)
>
> Mark
>
> On Wed, Feb 28, 2018 at 4:50 PM András Ferenc WACHA <
> wacha.and...@ttk.mta.hu> wrote:
>
> Dear Mahmood,
>
> as far as I know, each command supports the "-nobackup" command line
> switch...
>
> Best regards,
>
> Andras
>
>
> On 02/28/2018 04:46 PM, Mahmood Naderan wrote:
> > Hi,How can I disable the backup feature? I mean backed up files which
> start and end with # character.
> >
> > Regards,
> > Mahmood
>
> --
> András Ferenc Wacha, PhD
> research fellow, CREDO instrument responsible
>
> Biological Nanochemistry Research Group
>
> Institute of Materials and Environmental Chemistry
> Research Centre for Natural Sciences
> Hungarian Academy of Sciences (RCNS HAS)
> Magyar tudósok körútja 2.
> 
> H-1117 Budapest, Hungary
> 
> Phone: +36-1-382-6427
> Web: http://bionano.ttk.mta.hu,
> CREDO SAXS instrument: http://credo.ttk.mta.hu
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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Re: [gmx-users] cpu/gpu utilization

[Szilárd Páll]

Your run is probably GPU-bound because you have a rather slow GPU and as
per new mdrun defaults both PME and nonbondeds are offloaded which may not
be ideal for your case. Try the different offload modes to see which one is
best on your hardware.

Additionally, you still have not provided the *mdrun log file* I requested.
top output is not what I asked for.




--
Szilárd

On Wed, Feb 28, 2018 at 4:47 PM, Mahmood Naderan 
wrote:

> I forgot to say that gromacs reports
>
> No option -multi
> Using 1 MPI thread
> Using 16 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
>
> NOTE: GROMACS was configured without NVML support hence it can not exploit
>   application clocks of the detected Quadro M2000 GPU to improve
> performance.
>
>
>
>
>
>
> Regards,
> Mahmood
>
>
> On Wednesday, February 28, 2018, 7:15:13 PM GMT+3:30, Mahmood Naderan <
> nt_mahm...@yahoo.com> wrote:
>
>
> By runing
>
> gmx mdrun -nb gpu -deffnm md_0_1
>
>
> I see the following outputs
>
>
> $ top -b  | head -n 10
> top - 19:14:10 up 7 min,  1 user,  load average: 4.54, 1.40, 0.54
> Tasks: 344 total,   1 running, 343 sleeping,   0 stopped,   0 zombie
> %Cpu(s):  7.1 us,  0.5 sy,  0.0 ni, 91.9 id,  0.4 wa,  0.0 hi,  0.0 si,
> 0.0 st
> KiB Mem : 16438496 total, 13462876 free,  1968196 used,  1007424 buff/cache
> KiB Swap: 31250428 total, 31250428 free,0 used. 14054796 avail Mem
>
>   PID USER  PR  NIVIRTRESSHR S  %CPU %MEM TIME+ COMMAND
>  3604 mahmood   20   0 30.519g 525812 128788 S 918.8  3.2   6:58.38 gmx
>  1180 root  20   0  324688  69384  49712 S   6.2  0.4   0:14.41 Xorg
>  1450 mahmood   20   0  210228   7856   7192 S   6.2  0.0   0:00.17
> ibus-engin+
>
>
>
> $ nvidia-smi
> Wed Feb 28 19:14:35 2018
> +---
> --+
> | NVIDIA-SMI 384.81 Driver Version:
> 384.81|
> |---+--+
> --+
> | GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
> M. |
> |===+==+
> ==|
> |   0  Quadro M2000Off  | :23:00.0  On |
> N/A |
> | 65%   64CP058W /  75W |292MiB /  4035MiB | 93%
> Default |
> +---+--+
> --+
>
>
> +---
> --+
> | Processes:   GPU
> Memory |
> |  GPU   PID   Type   Process name
> Usage  |
> |===
> ==|
> |0  1180  G   /usr/lib/xorg/Xorg
> 141MiB |
> |0  1651  G   compiz
> 46MiB |
> |0  3604  C   gmx
> 90MiB |
> +---
> --+
>
>
>
>
>
> Any idea?
>
>
> Regards,
> Mahmood
>
>
> On Monday, February 26, 2018, 10:52:40 PM GMT+3:30, Szilárd Páll <
> pall.szil...@gmail.com> wrote:
>
>
> Hi,
>
> Please provide details, e.g. the full log so we know what version, on what
> hardware, settings etc. you're running.
>
>
>
> --
> Szilárd
>
>
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Re: [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

[Justin Lemkul]

On 2/28/18 1:13 PM, Marc Hoemberger wrote:

Hi everyone,

I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a
32-core node. The simulation worked well, however when I wanted to try to
run the identical simulation (same starting points etc) on a CPU/GPU node
the run crashes with two warnings of the following type:

WARNING: Listed nonbonded interaction between particles X and Y at distance
Z which is larger than the table limit W nm.

I know that my system is equilibrated well, and the same setup does work
perfect on the CPU only run.

For running the GPU run I use -ntomp 4 and one gpu, with -pin on. I use
CUDA 7.0.28 and gromacs 5.1.4 with plumed 2.4.0.

If there is any additional information that could help, let me know and I
will provide it.


Can you reproduce the problem with a vanilla GROMACS version 
(non-PLUMED), preferably something newer?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Backup files

[Mahmood Naderan]

Well I searched for "gromacs backoff" first and then while googling I saw [1] 
and an environment variable GMX_MAXBACKUP [2].

[1] http://cupnet.net/clean-gromacs-backups
[2] Environment Variables — GROMACS 5.1 documentation


Therefore I asked for a simpler method ;) 
 Anyway...

Regards,
Mahmood 

On Wednesday, February 28, 2018, 8:15:34 PM GMT+3:30, Mark Abraham 
 wrote:  
 
 There's an even better solution in the GROMACS documentation, which e.g. 
googling "disable gromacs backups" will find ;-)
Mark
On Wed, Feb 28, 2018 at 4:50 PM András Ferenc WACHA  
wrote:

Dear Mahmood,

as far as I know, each command supports the "-nobackup" command line
switch...

Best regards,

Andras


On 02/28/2018 04:46 PM, Mahmood Naderan wrote:
> Hi,How can I disable the backup feature? I mean backed up files which start 
> and end with # character.
>
> Regards,
> Mahmood

--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu,
CREDO SAXS instrument: http://credo.ttk.mta.hu


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[gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

[Marc Hoemberger]

Hi everyone,

I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a
32-core node. The simulation worked well, however when I wanted to try to
run the identical simulation (same starting points etc) on a CPU/GPU node
the run crashes with two warnings of the following type:

WARNING: Listed nonbonded interaction between particles X and Y at distance
Z which is larger than the table limit W nm.

I know that my system is equilibrated well, and the same setup does work
perfect on the CPU only run.

For running the GPU run I use -ntomp 4 and one gpu, with -pin on. I use
CUDA 7.0.28 and gromacs 5.1.4 with plumed 2.4.0.

If there is any additional information that could help, let me know and I
will provide it.

Best,
Marc
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Re: [gmx-users] Backup files

[Mark Abraham]

There's an even better solution in the GROMACS documentation, which e.g.
googling "disable gromacs backups" will find ;-)

Mark

On Wed, Feb 28, 2018 at 4:50 PM András Ferenc WACHA 
wrote:

> Dear Mahmood,
>
> as far as I know, each command supports the "-nobackup" command line
> switch...
>
> Best regards,
>
> Andras
>
>
> On 02/28/2018 04:46 PM, Mahmood Naderan wrote:
> > Hi,How can I disable the backup feature? I mean backed up files which
> start and end with # character.
> >
> > Regards,
> > Mahmood
>
> --
> András Ferenc Wacha, PhD
> research fellow, CREDO instrument responsible
>
> Biological Nanochemistry Research Group
>
> Institute of Materials and Environmental Chemistry
> Research Centre for Natural Sciences
> Hungarian Academy of Sciences (RCNS HAS)
> Magyar tudósok körútja 2.
> H-1117 Budapest, Hungary
> Phone: +36-1-382-6427 <+36%201%20382%206427>
> Web: http://bionano.ttk.mta.hu,
> CREDO SAXS instrument: http://credo.ttk.mta.hu
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] cpu/gpu utilization

[Mahmood Naderan]

I forgot to say that gromacs reports
No option -multi
Using 1 MPI thread
Using 16 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

NOTE: GROMACS was configured without NVML support hence it can not exploit
  application clocks of the detected Quadro M2000 GPU to improve 
performance.






Regards,
Mahmood 

On Wednesday, February 28, 2018, 7:15:13 PM GMT+3:30, Mahmood Naderan 
 wrote:  
 
 By runing
gmx mdrun -nb gpu -deffnm md_0_1

I see the following outputs

$ top -b  | head -n 10
top - 19:14:10 up 7 min,  1 user,  load average: 4.54, 1.40, 0.54
Tasks: 344 total,   1 running, 343 sleeping,   0 stopped,   0 zombie
%Cpu(s):  7.1 us,  0.5 sy,  0.0 ni, 91.9 id,  0.4 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem : 16438496 total, 13462876 free,  1968196 used,  1007424 buff/cache
KiB Swap: 31250428 total, 31250428 free,    0 used. 14054796 avail Mem 

  PID USER  PR  NI    VIRT    RES    SHR S  %CPU %MEM TIME+ COMMAND
 3604 mahmood   20   0 30.519g 525812 128788 S 918.8  3.2   6:58.38 gmx
 1180 root  20   0  324688  69384  49712 S   6.2  0.4   0:14.41 Xorg
 1450 mahmood   20   0  210228   7856   7192 S   6.2  0.0   0:00.17 ibus-engin+



$ nvidia-smi 
Wed Feb 28 19:14:35 2018   
+-+
| NVIDIA-SMI 384.81 Driver Version: 384.81    |
|---+--+--+
| GPU  Name    Persistence-M| Bus-Id    Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute M. |
|===+==+==|
|   0  Quadro M2000    Off  | :23:00.0  On |  N/A |
| 65%   64C    P0    58W /  75W |    292MiB /  4035MiB | 93%  Default |
+---+--+--+
   
+-+
| Processes:   GPU Memory |
|  GPU   PID   Type   Process name Usage  |
|=|
|    0  1180  G   /usr/lib/xorg/Xorg   141MiB |
|    0  1651  G   compiz    46MiB |
|    0  3604  C   gmx   90MiB |
+-+





Any idea?


Regards,
Mahmood 

On Monday, February 26, 2018, 10:52:40 PM GMT+3:30, Szilárd Páll 
 wrote:  
 
 Hi,
Please provide details, e.g. the full log so we know what version, on what 
hardware, settings etc. you're running.


--
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Re: [gmx-users] Backup files

[Mahmood Naderan]

Yes you are right. Thank you very much.


Regards,
Mahmood 

On Wednesday, February 28, 2018, 7:19:55 PM GMT+3:30, András Ferenc WACHA 
 wrote:  
 
 Dear Mahmood,

as far as I know, each command supports the "-nobackup" command line
switch...

Best regards,

Andras


  
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Re: [gmx-users] Backup files

[András Ferenc WACHA]

Dear Mahmood,

as far as I know, each command supports the "-nobackup" command line
switch...

Best regards,

Andras


On 02/28/2018 04:46 PM, Mahmood Naderan wrote:
> Hi,How can I disable the backup feature? I mean backed up files which start 
> and end with # character.
>
> Regards,
> Mahmood

-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
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[gmx-users] Backup files

[Mahmood Naderan]

Hi,How can I disable the backup feature? I mean backed up files which start and 
end with # character.

Regards,
Mahmood
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Re: [gmx-users] cpu/gpu utilization

[Mahmood Naderan]

By runing
gmx mdrun -nb gpu -deffnm md_0_1

I see the following outputs

$ top -b  | head -n 10
top - 19:14:10 up 7 min,  1 user,  load average: 4.54, 1.40, 0.54
Tasks: 344 total,   1 running, 343 sleeping,   0 stopped,   0 zombie
%Cpu(s):  7.1 us,  0.5 sy,  0.0 ni, 91.9 id,  0.4 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem : 16438496 total, 13462876 free,  1968196 used,  1007424 buff/cache
KiB Swap: 31250428 total, 31250428 free,    0 used. 14054796 avail Mem 

  PID USER  PR  NI    VIRT    RES    SHR S  %CPU %MEM TIME+ COMMAND
 3604 mahmood   20   0 30.519g 525812 128788 S 918.8  3.2   6:58.38 gmx
 1180 root  20   0  324688  69384  49712 S   6.2  0.4   0:14.41 Xorg
 1450 mahmood   20   0  210228   7856   7192 S   6.2  0.0   0:00.17 ibus-engin+



$ nvidia-smi 
Wed Feb 28 19:14:35 2018   
+-+
| NVIDIA-SMI 384.81 Driver Version: 384.81    |
|---+--+--+
| GPU  Name    Persistence-M| Bus-Id    Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute M. |
|===+==+==|
|   0  Quadro M2000    Off  | :23:00.0  On |  N/A |
| 65%   64C    P0    58W /  75W |    292MiB /  4035MiB | 93%  Default |
+---+--+--+
   
+-+
| Processes:   GPU Memory |
|  GPU   PID   Type   Process name Usage  |
|=|
|    0  1180  G   /usr/lib/xorg/Xorg   141MiB |
|    0  1651  G   compiz    46MiB |
|    0  3604  C   gmx   90MiB |
+-+





Any idea?


Regards,
Mahmood 

On Monday, February 26, 2018, 10:52:40 PM GMT+3:30, Szilárd Páll 
 wrote:  
 
 Hi,
Please provide details, e.g. the full log so we know what version, on what 
hardware, settings etc. you're running.


--
Szilárd
  
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Re: [gmx-users] generating Topology file of Metal Oxide

[André Farias de Moura]

It is doable, we have just finished a study (not published yet) of TiO2
nanoparticles oriented attachment.

But like Justin told you, GROMACS does not have any native support for that
kind of system, so you're on your own to build topologies and to extract
information from the trajectories (GROMACS has no built-in analysis tool
for crystalline solids whatsoever, although you might use some general
analysis like rdf/densities, electrostatic potential, etc.)

Andre

On Wed, Feb 28, 2018 at 10:04 AM, Justin Lemkul  wrote:

>
>
> On 2/28/18 7:14 AM, Kanwal Gill wrote:
>
>> Respected sir/ madam,
>>
>> I start MD silmulations with metal oxides but failed to generate its
>> topology file. i also checked with diferent softwares like PRODRG or ATB,
>> but do not get the topology file. please suggest me the solution.
>>
>
> GROMACS probably isn't the best software for such systems (you could make
> it work, but it would be pretty painful), and the built-in biomolecular
> force fields were definitely not designed to handle metal oxides, so it's
> no surprise that programs that generate GROMOS topologies would have failed.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
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_

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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] generating Topology file of Metal Oxide

[Justin Lemkul]

On 2/28/18 7:14 AM, Kanwal Gill wrote:

Respected sir/ madam,

I start MD silmulations with metal oxides but failed to generate its
topology file. i also checked with diferent softwares like PRODRG or ATB,
but do not get the topology file. please suggest me the solution.


GROMACS probably isn't the best software for such systems (you could 
make it work, but it would be pretty painful), and the built-in 
biomolecular force fields were definitely not designed to handle metal 
oxides, so it's no surprise that programs that generate GROMOS 
topologies would have failed.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] How to use LENNARD JONES 9-6 potential form in GROMACS

[Justin Lemkul]

On 2/28/18 12:15 AM, sanjeet kumar singh ch16d012 wrote:

Hello List,
  Can anyone tell me regarding how can i use Lennard Jones 9-6
potential form in GROMACS.


You can use a tabulated potential.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Equilibration

[Justin Lemkul]

On 2/28/18 6:38 AM, Amin Rouy wrote:

Thanks Justin, however,


I run a simulation of a solute in water. I have 2 question please:

1- After NVT equilibrium, I see that all quantities like
energies and
temperature become stable, except pressure. Should I continue
till pressure
also goes stable? or can I move forward and do it in
production run?


Pressure isn't a conserved quantity in NVT. It is in NPT (hence
the P).

Yes, but if a system goes to equilibrium in NVT, pressure should be 
fluctuating around a stable value.  For any system with defined N, T, 
V there should be one value for pressure, is not it?


Pressure fluctuates pretty wildly, and in NVT there is no barostat 
regulating it, so no, you should not expect to see any sort of stable 
value in this quantity.


-Justin


2- My interest production run is NVT, should I run
2th-step-equilibrium
with NPT also? or only NVT equilibration is enough?


Model whatever conditions are relevant to you; even with NVT, you
may want to simulate at a fixed density, which requires NPT
equilibration to stabilize the pressure/density and then continue
with NVT. Rarely is the initial configuration ideal.

-Justin

-- 
==


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu  | (540) 231-3129

http://www.biochem.vt.edu/people/faculty/JustinLemkul.html


==

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] generating Topology file of Metal Oxide

[Kanwal Gill]

Respected sir/ madam,

I start MD silmulations with metal oxides but failed to generate its
topology file. i also checked with diferent softwares like PRODRG or ATB,
but do not get the topology file. please suggest me the solution.

Kanwal.
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Re: [gmx-users] Equilibration

[Amin Rouy]

Thanks Justin, however,

>
>> I run a simulation of a solute in water. I have 2 question please:
>>
>> 1- After NVT equilibrium, I see that all quantities like energies and
>> temperature become stable, except pressure. Should I continue till
>> pressure
>> also goes stable? or can I move forward and do it in production run?
>>
>
> Pressure isn't a conserved quantity in NVT. It is in NPT (hence the P).
>
> Yes, but if a system goes to equilibrium in NVT, pressure should be
fluctuating around a stable value.  For any system with defined N, T, V
there should be one value for pressure, is not it?

> 2- My interest production run is NVT, should I run 2th-step-equilibrium
>> with NPT also? or only NVT equilibration is enough?
>>
>
> Model whatever conditions are relevant to you; even with NVT, you may want
> to simulate at a fixed density, which requires NPT equilibration to
> stabilize the pressure/density and then continue with NVT. Rarely is the
> initial configuration ideal.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] Equilibration

[Amin Rouy]

sorry but I did not get my answer.
In NVT equilibration, the pressure is not equilibrated yet, can I move
forward to production run? (I see that I have no blow up when I run
production)

On Wed, Feb 28, 2018 at 10:38 AM, Quyen V. Vu  wrote:

> No matter how many steps of equilibration you want to run.
> You need to run production run when your configuration is reasonable and in
> which condition, which ensemble you want to mimic
>
> On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy  wrote:
>
> > Hi,
> >
> >
> > I run a simulation of a solute in water. I have 2 questions please:
> >
> >
> > 1- After NVT equilibrium, I see that all quantities like energies and
> > temperature become stable, except pressure. Should I continue untill
> > pressure becomes stable too? or can I move forward and do it in
> > production run?
> >
> > 2- My interest production run is NVT, should I run
> > 2th-step-equilibrium with NPT also? or only NVT equilibration is
> > enough?
> >
> >
> > Thanks for answer
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> >
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Re: [gmx-users] Equilibration

[Quyen V. Vu]

No matter how many steps of equilibration you want to run.
You need to run production run when your configuration is reasonable and in
which condition, which ensemble you want to mimic

On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy  wrote:

> Hi,
>
>
> I run a simulation of a solute in water. I have 2 questions please:
>
>
> 1- After NVT equilibrium, I see that all quantities like energies and
> temperature become stable, except pressure. Should I continue untill
> pressure becomes stable too? or can I move forward and do it in
> production run?
>
> 2- My interest production run is NVT, should I run
> 2th-step-equilibrium with NPT also? or only NVT equilibration is
> enough?
>
>
> Thanks for answer
> --
> 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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[gmx-users] Equilibration

[Amin Rouy]

Hi,


I run a simulation of a solute in water. I have 2 questions please:


1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue untill
pressure becomes stable too? or can I move forward and do it in
production run?

2- My interest production run is NVT, should I run
2th-step-equilibrium with NPT also? or only NVT equilibration is
enough?


Thanks for answer
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[gmx-users] An atom is beyond the wall in gromacs2018

[Joel Awuah]

Hi Gromacs Users
I did a simulated annealing MD with gromacs/5.0.1 and gromacs/2018. In both
cases I had the same input configuration and parameters for the potential
wall. The simulation with gromacs/5.0.1 did achieve convergence but with
the gromacs/2018, an atom always go beyond the wall. Can someone please
help figure out what the problem with the gromacs/2018 one.

Cheers
Joel


-- 
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*Institute for Frontier Materials*

*Deakin University*
*Waurn Ponds, 3126 VIC*
*Australia +61450070635*
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