Re: [gmx-users] Onsager coefficient

[David van der Spoel]

Den 2020-03-30 kl. 22:51, skrev Sina Omrani:

Hi dear Gromacs users,
Sorry to ask again but I really appreciate the help on this subject.

thanks.

On Fri, 27 Mar 2020 at 02:23, Sina Omrani  wrote:


  Hi, I would like to calculate the Onsager coefficient but after months of
study, I'm not able to do that. if anybody can help me I would really
appreciate it. I don't know if there is a specific command to do it or it
needs a series of analyses.

P.S. I attached a picture of a formula that calculates the Onsager
coefficient from MD.

sincerely,
Sina Omrani

I see no attachment and google does not help either. What is an Onsager 
coefficient?


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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.

[gmx-users] Generating velocities

[Mohamed Abdelaal]

Hello everybody,

If my molecules are moving and I want to add the velocity, should I
generate the velocity through the .mdp file, or should I add the velocities
into my .gro file and insert the molecules?

Thanks,
Mohamed
-- 
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.

Re: [gmx-users] replica exchange simulations performance issues.

[Miro Astore]

I got up to 25-26 ns/day with my 4 replica system  (same logic scaled
up to 73 replicas) which I think is reasonable. Could I do better?

mpirun -np 48 gmx_mpi mdrun  -ntomp 1 -v -deffnm memb_prod1 -multidir
1 2 3 4 -replex 1000

 I have tried following the manual but I don't think i'm going it
right I keep getting errors. If you have a minute to suggest how I
could do this I would appreciate that.

log file accounting:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
On 12 MPI ranks Computing: Num Num Call Wall time Giga-Cycles Ranks
Threads Count (s) total sum %
-
Domain decomp. 12 1 26702 251.490 8731.137 1.5
DD comm. load 12 1 25740 1.210 42.003 0.0 DD
comm. bounds 12 1 26396 9.627 334.238 0.1
Neighbor search 12 1 25862 283.564 9844.652 1.7
Launch GPU ops. 12 1 5004002 343.309 11918.867 2.0
Comm. coord. 12 1 2476139 508.526 17654.811 3.0 Force 12 1 2502001
419.341 14558.495 2.5
Wait + Comm. F 12 1 2502001 347.752 12073.100 2.1
PME mesh 12 1 2502001 11721.893 406955.915 69.2
Wait Bonded GPU 12 1 2503 0.008 0.285 0.0
Wait GPU NB nonloc. 12 1 2502001 48.918 1698.317 0.3
Wait GPU NB local 12 1 2502001 19.475 676.141 0.1
NB X/F buffer ops. 12 1 9956280 753.489 26159.337 4.5
Write traj. 12 1 519 1.078 37.427 0.0 Update 12 1 2502001 434.272 15076.886 2.6
Constraints 12 1 2502001 701.800 24364.800 4.1
Comm. energies 12 1 125942 36.574 1269.776 0.2
Rest 1047.855 36378.988 6.2
-
Total 16930.182 587775.176 100.0
-
Breakdown of PME mesh computation
-
PME redist. X/F 12 1 5004002 1650.247 57292.604 9.7
PME spread 12 1 2502001 4133.126 143492.183 24.4
PME gather 12 1 2502001 2303.327 79965.968 13.6
PME 3D-FFT 12 1 5004002 2119.410 73580.828 12.5
PME 3D-FFT Comm. 12 1 5004002 918.318 31881.804 5.4
PME solve Elec 12 1 2502001 584.446 20290.548 3.5
 -

Best, Miro

On Tue, Mar 31, 2020 at 9:58 AM Szilárd Páll  wrote:
>
> On Sun, Mar 29, 2020 at 3:56 AM Miro Astore  wrote:
>
> > Hi everybody. I've been experimenting with REMD for my system running
> > on 48 cores with 4 gpus (I will need to scale up to 73 replicas
> > because this is a complicated system with many DOF I'm open to being
> > told this is all a silly idea).
> >
>
> It is a bad idea, you should have at least 1 physical core per replica and
> with a large system ideally more.
> However, if you are going for high efficiency (aggregate ns/day per phyical
> node), always put at least 2 replicas per GPU.
>
>
> >
> > My run configuration is
> > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11
> > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000
> >
> > the best I can squeeze out of this is 9ns/day. In a non-replica
> > simulation I can hit 50ns/day with a single GPU and 12 cores.
> >
>
> That is abnormal and indicates that:
> - either something is wrong with the hardware mapping / assignment in your
> run or; do use simply "-pin on" and let mdrun manage threads pinning (that
> map-by-numa is certainly not optimal); also I advise against tweaking the
> thread count and using weird numbers like 11 (just use quarter);
> - your exchange overhead is very high (check the communication cost in the
> log)
>
> If you share some log files of a standalone and a replex run, we can advise
> where the performance loss comes from.
>
> Cheers,
> --
> Szilárd
>
> Looking at my accounting, for a single replica 52% of time is being
> > spent on the "Force" category with 92% of my Mflops going into NxN
> > Ewald Elec. + LJ [F]
> >
>
> > I'm wondering what I could do to reduce this bottle neck if anything.
> >
> > Thank you.
> > --
> > Miro A. Astore   (he/him)
> > PhD Candidate | Computational Biophysics
> > Office 434 A28 School of Physics
> > University of Sydney
> > --
> > 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
>
> * 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.



-- 
Miro A. Astore   (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney
-- 
Gromacs Users mailing 

Re: [gmx-users] replica exchange simulations performance issues.

[Szilárd Páll]

On Sun, Mar 29, 2020 at 3:56 AM Miro Astore  wrote:

> Hi everybody. I've been experimenting with REMD for my system running
> on 48 cores with 4 gpus (I will need to scale up to 73 replicas
> because this is a complicated system with many DOF I'm open to being
> told this is all a silly idea).
>

It is a bad idea, you should have at least 1 physical core per replica and
with a large system ideally more.
However, if you are going for high efficiency (aggregate ns/day per phyical
node), always put at least 2 replicas per GPU.


>
> My run configuration is
> mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11
> -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000
>
> the best I can squeeze out of this is 9ns/day. In a non-replica
> simulation I can hit 50ns/day with a single GPU and 12 cores.
>

That is abnormal and indicates that:
- either something is wrong with the hardware mapping / assignment in your
run or; do use simply "-pin on" and let mdrun manage threads pinning (that
map-by-numa is certainly not optimal); also I advise against tweaking the
thread count and using weird numbers like 11 (just use quarter);
- your exchange overhead is very high (check the communication cost in the
log)

If you share some log files of a standalone and a replex run, we can advise
where the performance loss comes from.

Cheers,
--
Szilárd

Looking at my accounting, for a single replica 52% of time is being
> spent on the "Force" category with 92% of my Mflops going into NxN
> Ewald Elec. + LJ [F]
>

> I'm wondering what I could do to reduce this bottle neck if anything.
>
> Thank you.
> --
> Miro A. Astore   (he/him)
> PhD Candidate | Computational Biophysics
> Office 434 A28 School of Physics
> University of Sydney
> --
> 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

* 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.

Re: [gmx-users] Onsager coefficient

[Sina Omrani]

Hi dear Gromacs users,
Sorry to ask again but I really appreciate the help on this subject.

thanks.

On Fri, 27 Mar 2020 at 02:23, Sina Omrani  wrote:

>  Hi, I would like to calculate the Onsager coefficient but after months of
> study, I'm not able to do that. if anybody can help me I would really
> appreciate it. I don't know if there is a specific command to do it or it
> needs a series of analyses.
>
> P.S. I attached a picture of a formula that calculates the Onsager
> coefficient from MD.
>
> sincerely,
> Sina Omrani
>
-- 
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.

[gmx-users] GROMACS - tip7p itp and gro files - couldn't find them anywhere

[Jacek Artur Kozuch]

Hi all,

I've seen that recent tip7p water model 
(https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out. 
However, I couldn't find or I missed where the itp and gro files are deposited.

Anybody knows where to find them?

Thanks a lot in advance!

Best,
Jacek
[https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/jpcbfk/2019/jpcbfk.2019.123.issue-21/acs.jpcb.9b03149/20190523/images/large/jp-2019-03149k_0011.jpeg]
Seven-Site Effective Pair Potential for Simulating Liquid Water | The Journal 
of Physical Chemistry B
Constant pressure simulations were carried out to construct a new rigid 
nonpolarizable seven-site water model (TIP7P), which is an effective and 
efficient version of flexible seven-fluctuating-charge water model. In this 
model, the positive charges are located on three nuclei and the negative 
charges disperse on two bond sites at the geometric center of each OH bond and 
two lone-pair sites ...
pubs.acs.org




Dr. Jacek Kozuch
Postdoctoral Researcher - Boxer Lab

Stanford University
Department of Chemistry
Keck Science Building
380 Roth Way
Stanford, California 94305-5012
phone +1 (650) 723-0386
https://web.stanford.edu/group/boxer/


-- 
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.

[gmx-users] Coupled Gromacs+CP2K QM/MM user survey

[SINDT Julien]

Dear Gromacs users,

My name is Julien Sindt and I am a member of the BioExcel Centre of Excellence. 
We aim to provide support to academic and industrial researchers in the use of 
high-performance computing (HPC) and high-throughput computing (HTC) in 
biomolecular research (if you're interested, please check out 
bioexcel.eu). One of the projects we are working on is 
coupling Gromacs with the quantum chemistry package CP2K to enable QM/MM 
simulation of biomolecular systems -- we are working in close collaboration 
with the developers of Gromacs to create this feature and hope that it will be 
available soon.

We will support users of coupled Gromacs+CP2K on this mailing list and on the 
BioExcel QM/MM support forum at https://ask.bioexcel.eu/c/qmmm-biosim/. We've 
developed a survey to get a better idea of the interests and needs of the 
biomolecular simulation community with regards to QM/MM to help shape the user 
support and training that we provide, and very much welcome input from Gromacs 
users. If you would like a say in this, please contribute by filling out the 
survey here: https://bioexcel.eu/bioexcel-qm-mm-survey/  (deadline April 5th). 
The overall insights from the survey will be shared publicly later in the year.

If you have any further questions, please feel free to contact me, either on 
this mailing list or by emailing 
j.si...@epcc.ed.ac.uk.

Regards,
Julien


Dr Julien Sindt
HPC Applications Consultant, EPCC
2.20 The Bayes Centre
47 Potterrow
Edinburgh, EH8 9BT

Email: j.si...@epcc.ed.ac.uk
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.
-- 
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.

Re: [gmx-users] GROMACS 2019-rc1 install issues

[Paul bauer]

Also,

please don't use Release candidate versions for anything serious. 
Instead use the latest official release that suits you.


Cheers

Paul

On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote:

Hi everyone,

I'm a beginner user of GROMACS, and I'm having some troubles with the
installation. I follow the instruction in
http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html ,
but when i run "make", appear the error shown in file attached.
Any advice will be appreciated.

Regards,

Nicolas Rozas Castro
Universidad de Chile, Faculty of Science.



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

--
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.

Re: [gmx-users] GROMACS 2019-rc1 install issues

[Paul bauer]

Hello,

you can't attach files to the list here, either paste the error directly 
from the terminal or upload the file somewhere and share the link.


Cheers

Paul

On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote:

Hi everyone,

I'm a beginner user of GROMACS, and I'm having some troubles with the
installation. I follow the instruction in
http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html ,
but when i run "make", appear the error shown in file attached.
Any advice will be appreciated.

Regards,

Nicolas Rozas Castro
Universidad de Chile, Faculty of Science.



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

--
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.

Re: [gmx-users] Thin film drifting

[David van der Spoel]

Den 2020-03-29 kl. 22:46, skrev Alex:

On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel 
wrote:


Den 2020-03-29 kl. 19:43, skrev Alex:

Thanks.

On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel <

sp...@xray.bmc.uu.se>

wrote:


Den 2020-03-29 kl. 15:16, skrev Alex:

Thank Prof. van der Spoel for the response.
No, it isn't. The thin film is solid. There are interaction within the

thin

film and with water in the interface.

Please find a short movie of the unwrapped trajectory of the simulation

in

below link (water molecules are hidden); It shows minimization, then
equalization (NVT : tcoupl = v-rescale), then equalization (NpT :

tcoupl

=

v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl =
v-rescale and pcoupl = Parrinello-Rahman).

https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf

The thin film starts drifting significantly in the production along

both

x

and y directions.

Thanks, do you have isotropic pressure scaling?


Yes, the pcoupltype is isotropic. Please find the mdp file in below link.
https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa



Is the shift towards higher x and y values?


The shift is toward higher y value (+y).
It also firstly goes toward higher x value (+x ) for a very short time

and

then switches the direction to toward lower x value (-x) and finally

shifts

toward lower x value (-x).


But how is the solid modeled? Are there covalent bonds? It is not
certain there is a problem, at least I am not convinced. In P scaling
the coordinates of all particles are scaled by a constant and then
certain atoms can hop over PBC. If you plot the center of mass including
periodic boundaries (i.e. without unwrapping) it will be nicely in the
center of the box with few fluctuations. gmx traj may do this for you.


The thin film contains 1075 epoxy molecules in which there is no
inter-molecule covalent bond.
Below are the COM of the thin film with and without pbc in gmx traj.

I admit you are right and the comm-grps works fine as gmx traj -pbc yes
shows, thanks.
PBC : Yes
https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp

PBC: No
https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx
Note that the net movement is a lot smaller than the fluctuations in the 
in the one with PBC, I don't think there is any problem.






I and many others have done PMFs of small compounds over membranes of
different types, but not sure that anyone has noticed problems with
moving membranes.


I would also be so appreciated if you give me your preferences of the
following two choices I have in the PMF calculation of Mol_A to the
thin-film.
“comm-grps = *thin_film* *Mol_A* *SOL*”
or
“comm-grps = *Other* *SOL*”
Where the Other group contains the thin film and molecule A.



I would go for comm-grps = system.
Make sure to compute the pmf based on the relative distance between your 
compound and the membrane.



Best regards,
Alex





Maybe you can open an issue here:

https://gitlab.com/gromacs/gromacs/-/issues


I will open an issue.

Actually, in the later steps of the simulations, using umbrella sampling
and wham, I want to simulate the PMF a single molecule (called A; 26

atoms)

when it comes from water and diffuses inside the thin film till mid (com)
of thin film. pull_group1 and pull_group2 would be the Mol_A and

thin_film,

respectively.

I don't know if this kind of drifting would affect on the PMF, if so,

how?

If the comm-grps works I have the two following options to consider:
“comm-grps = thin_film Mol_A SOL”
or
“comm-grps = Other SOL”
Where the Other group contains the thin film and molecule A.
Which one do you recommend, please?

Thank you,
Alex





Best regards,
Alex

On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel <

sp...@xray.bmc.uu.se>

wrote:


Den 2020-03-29 kl. 05:24, skrev Alex:

Dear all,
In a system, I have a thin_film (infinitive in x-y directions) with

water

on top and bottom of it, PBC = xyz.
By the below flags I try to remove the motion of the center of mass

of

the

two group separately.
comm-grps = thin_film Water
comm-mode   = Linear
nstcomm = 100

However the thin film drift specially in x and y directions whereas I

was

expecting to have no drifting for the thin film, If I understood

correctly

the usage of the comm-grps!

Would you please let me know how I can stop drifting of the thin

film?


Thank you,
Alex


Is that a liquid film? Are there interactions within the film and with
water? The comm removal will calculate the center of mass taking
periodic boundaries into account so if your film moves one molecule

at a

time the COM will stay in place. In a realistic system the friction
between water and film should prevent this, hav eyou tried turning off
comm?

Historically this has been a fix for the Berendsen thermostat that
accumulates energy, however with a stochastic thermostat it should not
be necessary. Not sure about Nose-Hoover though.
--
David van 

[gmx-users] GROMACS 2019-rc1 install issues

[Nicolás Marcelo Rozas Castro]

Hi everyone,

I'm a beginner user of GROMACS, and I'm having some troubles with the
installation. I follow the instruction in
http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html ,
but when i run "make", appear the error shown in file attached.
Any advice will be appreciated.

Regards,

Nicolas Rozas Castro
Universidad de Chile, Faculty of Science.
-- 
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.

[gmx-users] gmx rdf (Angular Dependence)

[Farag, Hossam Mostafa Abdelhamid Mostafa]

Hi,

In the 2020.1 Release of Gromacs Documentation, it is written in page 486 the 
following:

"With gmx rdf (page 135) it is also possible to calculate an angle dependent 
rdf g_AB(r, theta), where the angle theta is defined with respect to a certain 
laboratory axis e, see Fig. 5.50 B"

However, when I go to "gmx rdf" command, I can't find any options to compute 
the anisotropic distribution.

I only found an option called -xy, which I am not sure how to use if this is 
the one relevant to what I am looking for.

Looking forward for your help.
Many thanks!
Hossam Farag
Graduate Research Assistant

Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
3614 Beckman Institute
405 N. Mathews Ave.
Urbana, IL 61801
217.418.3196 | hfar...@illinois.edu

[cid:e3f6c7fd-050f-4257-b3e1-c9207270e649]
-- 
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.