[gmx-users] Collision

[Mohamed Abdelaal]

Hello all,

I created a graphene sheet and performed energy minimization, after energy
minimization I found that parts of the graphene sheet was moved from the
box bottom to the box topside at the same place (as if it was translated
upwards). I looked online for the problem and I understood that I should
restrain the graphene sheet along the z axis. I did that using force =1000.
and the problem was solved and nothing moved.

After that I tried to insert 25 molecule of (C60) inside a box which
contains the graphene sheet. I did that and did the energy minimization but
part of the  graphene sheet moved again from its place although the maximum
force was less than 1000 which is the force I used to restrain the graphene
sheet. However I didn't have any error during the energy minimization. Does
this means that the problem is just in visualization or I might have a
problem in my energy minimization ?

It is also worth mentioning that the C60 molecules are not spherical as it
should be. I read about that and I found people mentioning that this shape
deformation in only a visualization problem and can be solved by using gmx
trjconv. is it possible that this problem has happened to my whole system
including the graphene sheet or it shouldn't affect my graphene sheet as
long as I have restrained it ?

more info:
I used   periodic_molecules = yes while trying to minimize my whole system.
(I also tried without it but no impact)
I wrote:

gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p
C60_GRM_box.top -o min1.tpr -maxwarn 2

followed by
gmx mdrun -v -deffnm min1

and I got the below result:
writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 3293 steps
Potential Energy  =  6.3598562e+05
Maximum force =  9.9486487e+02 on atom 12087
Norm of force =  6.5454323e+01

Can anybody help me please.

Thanks

Mohamed
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[gmx-users] How GROMACS can be compiled with subsystem Ubuntu 18.04 on Windows Server 2019 Standard?

[Kamil Rakowski]

How GROMACS can be compiled with subsystem Ubuntu 18.04 on Windows Server 2019 
Standard. Installed CUDA for win serwer 2019 and Windows drivers for Xeon Phi ( 
mpss 3.8.3).
I have Dell Poweredge R720 with: 1x Intel Xeon Phi 7120p, 2x Intel Xeon 
E-2695v2 and GPU Geforce RTX 2060 SUPER.
I don't know how to compile this configuration with cmake to run GROMACS with 
full performance.

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[gmx-users] uni axial deformation with semi-isotropic pressure coupling at 1 bar

[Pragati Sharma]

Dear all,

While using 'deform' option for elongation in Z direction, I have set the
compressibility  to  zero. Should I set pressure in z direction also zero
(ref_p =0 ) or 1  in that direction.

I need to extract -Pzz for plotting stress-strain.

Thanks
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Re: [gmx-users] error on graphene sheet simulation

[John Whittaker]

Hi,

That tutorial is not from the GROMACS team, it is provided by a user.

Anyway, something is wrong with your topology. The CHARMM forcefield used
in that tutorial has the atomtype CG2R61 available, so it should be
defined in your topology as long as you include the CHARMM36 forcefield.

Can you copy/paste the contents of your topology in a reply?

- John

> while going through your tutorial on graphene sheet i was facing an error.
> https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/
>
> NOTE 2 [file nvt.mdp]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
>
> Setting the LD random seed to 164492569
> Generated 20503 of the 20503 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17396 of the 20503 1-4 parameter combinations
>
> ERROR 1 [file GRA.itp, line 7]:
>   Atomtype CG2R61 not found
>
>
> There were 2 notes
>
> ---
> Program: gmx grompp, version 2019.1
> Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1333)
>
> Fatal error:
> There was 1 error in input file(s)
>
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> can you give any suggestion what could have gone wrong...
> thanks
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Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Andreas Baer]

Hi,

sorry for it!
https://faubox.rrze.uni-erlangen.de/getlink/fiUpELsXokQr3a7vyeDSKdY3/benchmarks_2019-2020_all

Cheers,
Andreas

On 27.02.20 17:59, Szilárd Páll wrote:
On Thu, Feb 27, 2020 at 1:08 PM Andreas Baer > wrote:


Hi,

On 27.02.20 12:34, Szilárd Páll wrote:
> Hi
>
> On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer
mailto:andreas.b...@fau.de>> wrote:
>
>> Hi,
>>
>> with the link below, additional log files for runs with 1 GPU
should be
>> accessible now.
>>
> I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun
-ntmpi 1.
>
> It would also help if you could share some input files in case
if further
> testing is needed.
Ok, there is now also an additional benchmark with `-ntmpi 1 -ntomp 4
-bonded gpu -update gpu` as parameters. However, it is run on the
same
machine with smt disabled.
With the following link, I provide all the tests on this machine,
I did
by now, along with a summary of the performance for the several input
parameters (both in `logfiles`), as well as input files
(`C60xh.7z`) and
the scripts to run these.


Links seems to be missing.
--
Szilárd

I hope, this helps. If there is anything else, I can do to help,
please
let me know!
>
>
>> Thank you for the comment with the rlist, I did not know, that
this will
>> affect the performance negatively.
>
> It does in multiple ways. First, you are using a rather long
list buffer
> which will make the nonbonded pair-interaction calculation more
> computational expensive than it could be if you just used a
tolerance and
> let the buffer be calculated. Secondly, as setting a manual
rlist disables
> the automated verlet buffer calculation, it prevents mdrun from
using a
> dual pairl-list setup (see
>

http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning)
> which has additional performance benefits.
Ok, thank you for the explanation!
>
> Cheers,
> --
> Szilárd
Cheers,
Andreas
>
>
>
>> I know, about the nstcalcenergy, but
>> I need it for several of my simulations.
> Cheers,
>> Andreas
>>
>> On 26.02.20 16:50, Szilárd Páll wrote:
>>> 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
mailto:andreas.b...@fau.de>>
>> 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
>>>

[gmx-users] GROMACS 2019.6 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.6 is available!

The sixth patch release fixes several issues found since the previous 
patch release of GROMACS 2019.

We encourage all users of the 2019 series to update to 2019.6.
Please see the link to the release notes below for more details.

Please note that the 2019 branch is now out of main support, and we will 
only address critical scientific issues in this branch.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.6.tar.gz
Documentation: http://manual.gromacs.org/2019.6/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.6.tar.gz

Happy simulating!

Paul

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GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] error on graphene sheet simulation

[Devargya Chakraborty]

while going through your tutorial on graphene sheet i was facing an error.
https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/

NOTE 2 [file nvt.mdp]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

Setting the LD random seed to 164492569
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations

ERROR 1 [file GRA.itp, line 7]:
  Atomtype CG2R61 not found


There were 2 notes

---
Program: gmx grompp, version 2019.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1333)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

can you give any suggestion what could have gone wrong...
thanks
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