Re: [gmx-users] Not enough memory. Failed to calloc :

[Mark Abraham]

You don't have enough memory ;-) get more, or do a smaller task

Mark

On Thu, 21 Jan 2016 11:51 Nikhil Maroli  wrote:

> Dear all,
> i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system
> with a total of 60686 atoms including water,ions and proteins,
> it ended up with the following error
>
> Fatal error:
> Not enough memory. Failed to calloc -1082130432 elements of size 4 for
> grps[j].nm_ind
> (called from file
>
> /home/rajendra/software/gromacs_source/gromacs-5.0.5/src/gromacs/fileio/tpxio.c,
> line 2510)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Kindly advice me the on this problem
>
>
> --
> Ragards,
> Nikhil Maroli
> --
> Gromacs Users mailing list
>
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[gmx-users] Error bar of order parameter

[m g]

Dear Justin,
in order to calculate the error bar for order parameter, i can't understand, 
which command exactly must be used? g_covar?g_anaeig? is it output of these 
commands?
Many thanks
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Re: [gmx-users] Constraints errors

[Justin Lemkul]

On 1/20/16 11:16 PM, Alireza Moradzadeh wrote:

Dear Users,
I want to simulate [BMIM][PF6] using following itp
[ moleculetype ]
PF6 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 P 1 PF6 P1 1 1.13 30.974
2 FP 1 PF6 F2 2 -0.33 18.998
3 FP 1 PF6 F3 3 -0.33 18.998
4 FP 1 PF6 F4 4 -0.33 18.998
5 FP 1 PF6 F5 5 -0.33 18.998
6 FP 1 PF6 F6 6 -0.33 18.998
7 FP 1 PF6 F7 7 -0.33 18.998
[ bonds ]
1 2 1
1 3 1
1 4 1
1 5 1
1 6 1
1 7 1
[ angles ]
2 1 3 1
2 1 4 1
2 1 6 1
2 1 7 1
3 1 4 1
3 1 5 1
3 1 7 1
4 1 5 1
4 1 6 1
5 1 6 1
5 1 7 1
6 1 7 1
2 1 5 1 180. 1165.
3 1 6 1 180. 1165.
4 1 7 1 180. 1165.

But I get following errors for both of my molecules.

Molecule type "PF" has 21 constraints.
For stability and efficiency reasons there should not be more constraints
more than internal degree of freedoms: 15
Is it right to use maxwarn in this case?!



You're being told that what you're trying to do (presumably via constraints = 
all-angles) is not physically stable.  You can override this, of course, but 
then don't come asking for help when your simulation crashes.  grompp already 
warned you :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Error bar of order parameter

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 1/21/16 8:23 AM, m g wrote:

Dear Justin,

  I want to calculate the error bar for deuterium order parameter data for acyl
chains of DPPC, for each carbons. I can calculate the Scd, i was learned it from
your tutorial. but i don't know how can i get error bar for deuterium order
parameter of each carbons. for example like this figure that attached. would you
please help me?



I already told you how to do this.  Either compute these values from independent 
simulations, and average those values and obtain a standard deviation, or run 
gmx order with -b and -e and average over blocks of time and obtain a standard 
error.


-Justin



On Thursday, January 21, 2016 4:40 PM, Justin Lemkul  wrote:




On 1/21/16 8:03 AM, m g wrote:
 > Dear Justin,
 > in order to calculate the error bar for order parameter, i can't understand,
which command exactly must be used? g_covar?g_anaeig? is it output of these
commands?

"Order parameter" is ambiguous.  What are you actually trying to do?  After
reading about all available commands in the manual, what do you learn?


-Justin


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  |
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Not enough memory. Failed to calloc :

[Nikhil Maroli]

Dear all,
i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system
with a total of 60686 atoms including water,ions and proteins,
it ended up with the following error

Fatal error:
Not enough memory. Failed to calloc -1082130432 elements of size 4 for
grps[j].nm_ind
(called from file
/home/rajendra/software/gromacs_source/gromacs-5.0.5/src/gromacs/fileio/tpxio.c,
line 2510)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Kindly advice me the on this problem


-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] Error bar of order parameter

[Justin Lemkul]

On 1/21/16 8:03 AM, m g wrote:

Dear Justin,
in order to calculate the error bar for order parameter, i can't understand, 
which command exactly must be used? g_covar?g_anaeig? is it output of these 
commands?


"Order parameter" is ambiguous.  What are you actually trying to do?  After 
reading about all available commands in the manual, what do you learn?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Not enough memory. Failed to calloc :

[Justin Lemkul]

On 1/21/16 5:50 AM, Nikhil Maroli wrote:

Dear all,
i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system
with a total of 60686 atoms including water,ions and proteins,
it ended up with the following error

Fatal error:
Not enough memory. Failed to calloc -1082130432 elements of size 4 for
grps[j].nm_ind
(called from file
/home/rajendra/software/gromacs_source/gromacs-5.0.5/src/gromacs/fileio/tpxio.c,
line 2510)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Kindly advice me the on this problem



Water and ions should not be part of an MM/PBSA calculation.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Not enough memory. Failed to calloc :

[Nikhil Maroli]

Thanks to Mark and Justin,
my protein contains around 8000 atoms and ligand is around 33 atoms,and i 
used united atom ff,
my workstation is with 64GB ram,but when i run the g_mmpbsa,i observed in  
performance monitor that there is no rise in memory usage,if it is 
shortage of memory is there any possibility to see how much more is 
required to run this so that i can upgrade it,:) (Why i concerned is if it 
is over the limit of motherboard i can go for another system instead of 
upgrading present one)

Thanks

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[gmx-users] trivial question about water molecules

[Marta Wisniewska]

Hello Gromacs Users;

I'd like to calculate the # of replaced water molecules by sodium chloride
in my system . I added a 0.15M concentration of NaCl. How can I calculate
the number of water molecules, which are replaced by ions?

Thank you in advance,
Marta
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Re: [gmx-users] Not enough memory. Failed to calloc :

[Mark Abraham]

Hi,

The memory use won't rise if there's a single large allocation that fails.
The large negative number present in the error message indicates that the
amount of memory asked for exceeded 2^31 bytes (because the quantity was
larger than a signed 4-byte integer), which is unreasonable. You have to
figure out how your usage is leading to a large request (and maybe read the
g_mmpbsa docs, or ask the person who actually develops g_mmpbsa, who isn't
on the GROMACS team).

Mark

On Thu, Jan 21, 2016 at 4:59 PM Nikhil Maroli  wrote:

> Thanks to Mark and Justin,
> my protein contains around 8000 atoms and ligand is around 33 atoms,and i
> used united atom ff,
> my workstation is with 64GB ram,but when i run the g_mmpbsa,i observed in
> performance monitor that there is no rise in memory usage,if it is
> shortage of memory is there any possibility to see how much more is
> required to run this so that i can upgrade it,:) (Why i concerned is if it
> is over the limit of motherboard i can go for another system instead of
> upgrading present one)
>
> Thanks
>
> --
> Gromacs Users mailing list
>
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> posting!
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Re: [gmx-users] trivial question about water molecules

[Smith, Micholas D.]

Check the original topology file without ions for the line SOL(number of 
water's here)

then check the new topology file with ions-added  for the same line and 
compare. 


===
Micholas Dean Smith, PhD.
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 Marta 
Wisniewska 
Sent: Thursday, January 21, 2016 11:47 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] trivial question about water molecules

Hello Gromacs Users;

I'd like to calculate the # of replaced water molecules by sodium chloride
in my system . I added a 0.15M concentration of NaCl. How can I calculate
the number of water molecules, which are replaced by ions?

Thank you in advance,
Marta
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Re: [gmx-users] trivial question about water molecules

[Justin Lemkul]

On 1/21/16 11:47 AM, Marta Wisniewska wrote:

Hello Gromacs Users;

I'd like to calculate the # of replaced water molecules by sodium chloride
in my system . I added a 0.15M concentration of NaCl. How can I calculate
the number of water molecules, which are replaced by ions?



genion replaces a water molecule with an ion, so the number of waters replaced 
equals the number of ions added.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] GROMACS performance with an NVidia Tesla k40c

[Szilárd Páll]

Hi,

On Wed, Jan 20, 2016 at 6:35 PM, Michail Palaiokostas Avramidis
 wrote:
> Hi,
>
> thanks for your answer. :) I tried to attach in the previous email
> the log file but for some reason it never arrived on the list. Actually I 
> searched a bit more and the speed up reaches the theoretical maximum reported 
> by Nvidia so probably I shouldn't be greedy.

You can be greedy, but it's best to stay reasonable.

Nitpick: I doubt NVIDIA reported a "theoretical maximum", more likely
an observed one. The theoretical maximum could be as high as ~5x (or a
bit more) depending on simulation system/settings, but that will
happen only under special circumstances (e.g. no constraints or
unusually long cut-off). Of course you can also turn off
architecture-optimized CPU kernels and get huge speedup  ;)

A few suggestions that _may_ give a bit of improvement, but don't
expect at most a few %:
- try a few other nstlist values, e.g. 50, 75 (<40 will likely not help)
- your LINCS setting are somewhat conservative (lincs-iter=2 is
recommended for NVE or minimization), you can use the default
lincs-iter=1 which will as a side-effect allow a bit more CPU-GPU
overlap.

If you get lucky, the load balancer may switch to one step coarser PME
grid (40 40 36) and get better GPU utilization.

Note that when you do performance measurements in short runs you
should always reset the performance counters to exclude the initial
load-balancing affect the reported timings (use -resethway or
-resetstep N).

Cheers,
--
Szilárd

> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Szilárd Páll 
> 
> Sent: Tuesday, January 19, 2016 9:05 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] GROMACS performance with an NVidia Tesla k40c
>
> Hi,
>
>
> On Tue, Jan 19, 2016 at 8:34 PM, Michail Palaiokostas Avramidis <
> m.palaiokos...@qmul.ac.uk> wrote:
>
>> Dear GMX users,
>>
>>
>> I have recently installed an Nvidia Tesla K40c in my workstation (already
>> had a quadro k2000) and I am currently trying to optimize its usage with
>> GROMACS. I used two compilations of GROMACS, one is the standard one as
>> suggested in the beginning of the installation documentation and one where
>> I added some more flags to see what will happen. The latter compilation
>> used:
>>
>>
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
>> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5
>> -DNVML_INCLUDE_DIR=/usr/include/nvidia/gdk
>> -DNVML_LIBRARY=/usr/lib/nvidia-352/libnvidia-ml.so
>>
>>
> Looks reasonable.
>
>
>>
>> So far I used 4 different combinations to test a water-membrane system of
>> ~30500 atoms for 5000 steps:
>>
>> 1) CPU only,
>>
>> 2) CPU+2GPUs (the default),
>>
>> 3) CPU+Quadro and
>>
>> 4) CPU+Tesla.
>>
>> Obviously the fastest is the Tesla one with 31ns/day. This is 3.6 times
>> faster than the CPU-only setup.
>>
>>
>> While this is good, I am not entirely satisfied with the speed-up. Do you
>> think is normal? Would you expect more?
>>
>
> 3.6x is perfectly normal; the typical GPU acceleration improvement is 2-4x.
>
> What makes you unsatisfied; why do you expect more speedup? (If you happen
> to be comparing to the speedup of other MD packages, do consider that
> GROMACS has highly optimized SIMD CPU kernels which makes it quite fast on
> CPUs only. With an already highly optimized baseline it's harder get high
> speedup, no matter what kind of accelerator you use.
>
>
>> One thing I noticed is that there was absolutely no difference with using
>> the custom, GPU-oriented compilation of GROMACS. Did I miss something there?
>>
>
> Not sure what you're referring to here, could you clarify?
>
>
>> The second thing I noticed is that even by increasing nstlist the
>> performance remained the same (despite the suggestion in the documentation).
>>
>
> Increasing from what value to what value? Note that mdrun will by default
> increase nstlist if the initial value is small.
> See Table 2 and related text in http://doi.wiley.com/10.1002/jcc.24030.
>
> Finally, in my log file I got the message (the actual log is attached to
>> the message):
>>
>> Force evaluation time GPU/CPU: 2.232 ms/3.189 ms = 0.700
>>
>> For optimal performance this ratio should be close to 1!
>>
>> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>> performance loss.
>>
>>
>> Can you please help me solve this imbalance? At the moment I am executing
>> gromacs with: gmx mdrun -v -deffnm npt-ini -gpu_id 0
>>
>
> The automated CPU-GPU load balancer should address this on its own - if
> possible. If your CPU is relatively slow, there is often not much more to
> do.
>
> Post log files of your runs and we may be able to suggest more.
>
> Cheers,
> --
> Szilárd
>
> Thank you in advance for your help.
>>
>>
>> Best Regards,
>>
>> Michail
>>
>>
>> 

[gmx-users] Contact_Angles_Calculation

[HZJ]

Dear GMX users,


Recently, I want to analyze the contact angle of a gas bubble adsorbed on a 
surface, during the simulation, 
the bubbule can move freely on the surface. I aim to calculate the contact 
angle for each frame. Did anyone
do such analysis and suggest a simple way to do it? I read some paper, one 
method is to calculate the 2D density of the bubble, and then to fit the edges 
of the curve to a function type and then get the angle. It seems this method is 
simple only for one frame. Thanks!



Best wishes!


Dr. He
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Re: [gmx-users] Contact_Angles_Calculation

[Michael Shirts]

See:

http://pubs.acs.org/doi/abs/10.1021/acs.langmuir.5b00842

For a study using GROMACS.  They code can be downloaded (though it
might not be trivial to use).

On Thu, Jan 21, 2016 at 6:32 PM, HZJ <1047334...@qq.com> wrote:
> Dear GMX users,
>
>
> Recently, I want to analyze the contact angle of a gas bubble adsorbed on a 
> surface, during the simulation,
> the bubbule can move freely on the surface. I aim to calculate the contact 
> angle for each frame. Did anyone
> do such analysis and suggest a simple way to do it? I read some paper, one 
> method is to calculate the 2D density of the bubble, and then to fit the 
> edges of the curve to a function type and then get the angle. It seems this 
> method is simple only for one frame. Thanks!
>
>
>
> Best wishes!
>
>
> Dr. He
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[gmx-users] Umbrella Sampling, Analysis Step

[Misa Banno]

Dear Gromacs users,

I've run the umbrella sampling. I could draw histograms with sufficient 
overlap, so I determined all of the simulations reached enough length of 
time. Now it's the analysis step.


When I chose tpr files and pullf.xvg (forces) files as the input to 
wham, I was able to analyze and draw PMF curve previously.


However, I chose tpr files and pullx.xvg (coordinates) files, I couldn't.
The command line is below.


gmx wham -it tpr-files.dat -ix pullx-files.dat  -o -hist -unit kCal -b 5 -e 
20


I got the profile.xvg but all PMF values are zero in that file.

While running gmx wham, I was getting warnings like below.
Warning, poor sampling bin 199 (z=-1.00185). Check your histograms!

I did simulation by using following COM pulling options:
; COM PULLING
pull = umbrella
pull_geometry= cylinder
pull_dim = N N Y
pull_r1  = 2
pull_r0  = 3
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 100
pull_nstfout = 100
pull_ngroups = 2
pull-ncoords = 1
pull-group1-name = zpopc
pull-group2-name = Protein
pull-coord1-groups   = 1 2
pull-coord1-origin   = 0 0 0
pull-coord1-vec  = 0 0 -1.0
pull-coord1-init = 0
pull-coord1-rate = 0
pull-coord1-k= 1000
pull-coord1-kB   = 0


Please help me in this regard.

Many Thanks
Misa Banno

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Re: [gmx-users] Contact_Angles_Calculation

[HZJ]

Thanks. I have come across this paper. It introduce how to calculate this 
angle. No code is provided with this
paper. Can they share this code? I use a smooth surface.


Best wishes!





-- Original --
From:  "Michael Shirts";;
Date:  Fri, Jan 22, 2016 11:40 AM
To:  "Discussion list for GROMACS users"; 
Cc:  "gromacs.org_gmx-users"; 
Subject:  Re: [gmx-users] Contact_Angles_Calculation



See:

http://pubs.acs.org/doi/abs/10.1021/acs.langmuir.5b00842

For a study using GROMACS.  They code can be downloaded (though it
might not be trivial to use).

On Thu, Jan 21, 2016 at 6:32 PM, HZJ <1047334...@qq.com> wrote:
> Dear GMX users,
>
>
> Recently, I want to analyze the contact angle of a gas bubble adsorbed on a 
> surface, during the simulation,
> the bubbule can move freely on the surface. I aim to calculate the contact 
> angle for each frame. Did anyone
> do such analysis and suggest a simple way to do it? I read some paper, one 
> method is to calculate the 2D density of the bubble, and then to fit the 
> edges of the curve to a function type and then get the angle. It seems this 
> method is simple only for one frame. Thanks!
>
>
>
> Best wishes!
>
>
> Dr. He
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Contact_Angles_Calculation

[Michael Shirts]

I believe the last line of the paper is: "We have made the code used
for this analysis available on the GitHub site:
https://github.com/shirtsgroup/droplet-analysis.;

On Thu, Jan 21, 2016 at 10:02 PM, HZJ <1047334...@qq.com> wrote:
> Thanks. I have come across this paper. It introduce how to calculate this 
> angle. No code is provided with this
> paper. Can they share this code? I use a smooth surface.
>
>
> Best wishes!
>
>
>
>
>
> -- Original --
> From:  "Michael Shirts";;
> Date:  Fri, Jan 22, 2016 11:40 AM
> To:  "Discussion list for GROMACS users";
> Cc:  "gromacs.org_gmx-users";
> Subject:  Re: [gmx-users] Contact_Angles_Calculation
>
>
>
> See:
>
> http://pubs.acs.org/doi/abs/10.1021/acs.langmuir.5b00842
>
> For a study using GROMACS.  They code can be downloaded (though it
> might not be trivial to use).
>
> On Thu, Jan 21, 2016 at 6:32 PM, HZJ <1047334...@qq.com> wrote:
>> Dear GMX users,
>>
>>
>> Recently, I want to analyze the contact angle of a gas bubble adsorbed on a 
>> surface, during the simulation,
>> the bubbule can move freely on the surface. I aim to calculate the contact 
>> angle for each frame. Did anyone
>> do such analysis and suggest a simple way to do it? I read some paper, one 
>> method is to calculate the 2D density of the bubble, and then to fit the 
>> edges of the curve to a function type and then get the angle. It seems this 
>> method is simple only for one frame. Thanks!
>>
>>
>>
>> Best wishes!
>>
>>
>> Dr. He
>> --
>> 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 send a 
>> mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
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