Re: [gmx-users] Visualize replica exchange

[Christian Blau]

Hi Ahmed,


I don't know about VMD, but you can try

./gromacs/scripts/demux.pl


Best,

Christian

On 2020-01-09 15:01, hind ahmed wrote:

Dear All,

How can I visualize replica exchange in VMD?

Thanks

--
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 probabilities and extend simulation

[Christian Blau]

Hi Ahmed,


If you have a look into "Optimal temperature ladders in replica exchange 
simulations", available here:

https://www.sciencedirect.com/science/article/pii/S000926140900356X

you will see that your exchange probabilities should be a bit higher. Then again, you might have to set up a lot more 
simulations, which you can get around with more advanced protocols like solute tempering (REST). These methods are 
implemented in PLUMED for example.



If you want further insight, I suggest using

demux.pl md.log

It's a good sign if you see single replicas walking through the whole temperature range, it's a bad sign if you see that 
some replicas only stay close to a certain temperature.



Best,

Christian


On 2020-01-09 14:58, hind ahmed wrote:

Dear All,

  Are these probabilities good? and how can I extend the simulation of 
replica-exchange?

Thanks

Replica exchange statistics
Repl  14999 attempts, 7500 odd, 7499 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  
.01  .01  .01  .01  .01  .01  .01  .01  .02  .02  .02  .01  .02  .02  .02  .02  
.02
Repl  number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  259  263  270  330   62   57   63   58   65   67   71   74   89   87  
 88  103  100  103   98   98  114   93  132  127  149  111  117  126  129  124  
145
Repl  average number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  
.01  .01  .01  .01  .01  .01  .02  .01  .02  .02  .02  .01  .02  .02  .02  .02  
.02


--
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] Make index command in gromacs

[Shan Jayasinghe]

Dear Gromacs Users,

Thank you very much for your valuable answers.

On Wed, Jan 8, 2020 at 8:40 PM Christian Blau  wrote:

> Hi Shan,
>
>
> gmx select gives you many more options to do complex arithmetic with
> selections that might help you here.
>
>
> You can try using
>
> gmx select -select "SELECTION STING"
>
> you'll find lots of selection string examples at the bottom in here:
>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
>
>
>
> Best,
>
> Christian
>
>
> On 2020-01-07 23:33, Shan Jayasinghe wrote:
> > Dear Gromacs Users,
> >
> > In my simulations, I have different sizes of water droplets.  I need
> > indexes of water molecules in each droplet separately. I am trying to
> make
> > the  index file with gmx make_ndx, but I couldn't do it. Appreciate your
> > help regarding this matter.
> >
> > Thank you.
> --
> 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.
>


-- 
Best Regards
Shan Jayasinghe
-- 
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_topolbuild error

[aayattimg]

I am getting error in topolbuild:
Fatal error.
Source code file: readmol2.c, line: 693
Atom 1 (O5') has 2 connections when allowed 0
 I have used the command
./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
tripos97
.mol2 file that I am using is as follows:
@MOLECULE
QCH
   3031 1 0 1
SMALL
USER_CHARGES
@ATOM
  1 O5'-1.9382342.2216390.669368 O 1 QCH  
-0.6458 
  2 H5T-2.1610903.0855150.989879 H 1 QCH   
0.4497 
  3 O3'-3.459429   -1.7287890.016186 O 1 QCH  
-0.6852 
  4 H3T-3.700920   -2.3239170.713748 H 1 QCH   
0.4392 
  5 C1'-0.662286   -0.787261   -0.296578 C 1 QCH   
0.3964 
  6 H1'-0.605691   -1.741658   -0.791073 H 1 QCH   
0.0394 
  7 C2'-1.435951   -0.8508841.016075 C 1 QCH  
-0.0947 
  8 H2'1   -1.108767   -0.0641591.683744 H 1 QCH   
0.0480 
  9 H2'2   -1.331556   -1.8073051.511592 H 1 QCH   
0.0480 
 10 C3'-2.859368   -0.5759970.536996 C 1 QCH   
0.2991 
 11 H3'-3.474441   -0.1270331.307751 H 1 QCH   
0.0153 
 12 C4'-2.6446200.372686   -0.650794 C 1 QCH   
0.1743 
 13 H4'-3.3101490.087545   -1.452894 H 1 QCH   
0.0890 
 14 C5'-2.8289241.845500   -0.355885 C 1 QCH   
0.0150 
 15 H5'1   -2.6332602.416008   -1.257986 H 1 QCH   
0.0776 
 16 H5'2   -3.8587552.018514   -0.059368 H 1 QCH   
0.0776 
 17 O4'-1.3046320.148647   -1.085285 O 1 QCH  
-0.4154 
 18 N1  0.746765   -0.330172   -0.139522 N 1 QCH  
-0.0020 
 19 C6  1.0374810.982281   -0.067547 C 1 QCH  
-0.1180 
 20 H6  0.1890231.636860   -0.090671 H 1 QCH   
0.2766 
 21 C5  2.3034181.4591660.033557 C 1 QCH  
-0.2943 
 22 H5  2.5017892.5095650.085307 H 1 QCH   
0.1984 
 23 C4  3.3551900.5215320.053970 C 1 QCH   
0.4864 
 24 N4  4.6248250.8606340.131082 N 1 QCH  
-0.8725 
 25 H41 5.3626320.1898710.139293 H 1 QCH   
0.4651 
 26 H42 4.8875511.8213770.170549 H 1 QCH   
0.4651 
 27 N3  3.028239   -0.778715   -0.004253 N 1 QCH  
-0.2232 
 28 H3  3.730821   -1.4912290.018101 H 1 QCH   
0.3215 
 29 C2  1.731998   -1.290150   -0.085103 C 1 QCH   
0.4517 
 30 O2  1.543842   -2.458176   -0.098679 O 1 QCH  
-0.4823 
@BOND
1 1 2 1
2 114 1
3 3 4 1
4 310 1
5 5 6 1
6 5 7 1
7 517 1
8 518 1
9 7 8 1
   10 7 9 1
   11 710 1
   121011 1
   131012 1
   141213 1
   151214 1
   161217 1
   171415 1
   181416 1
   191819 1
   201829 1
   211920 1
   221921 1
   232122 1
   242123 1
   252324 1
   262327 1
   272425 1
   282426 1
   292728 1
   302729 1
   312930 1
@SUBSTRUCTURE
  1  QCH  1    0   




kindly suggest to debug the error.
Thanking you in advance.

-- 
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] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thankyou!

On Fri, Jan 10, 2020 at 6:00 AM Justin Lemkul  wrote:

>
>
> On 1/9/20 9:42 AM, Navneet Kumar wrote:
> > Thank You, sir!
> >
> > What If I want to extend the residues like choose c-alpha of 150-200 &
> > 60-70 in a single index group ?
>
> 3 & r 60-70 | 3 & r 150-200
>
> Type "help" at the make_ndx prompt for examples of how to use the program.
>
> -Justin
>
> >
> > On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul  wrote:
> >
> >>
> >> On 1/8/20 4:49 AM, Christian Blau wrote:
> >>> Hi Navnett,
> >>>
> >>>
> >>> gmx select will be your friend.
> >>>
> >>>
> >>> At the bottom of
> >>>
> >>>
> >>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >>>
> >>> you'll find some example commands. Something along the lines of
> >>>
> >>>gmx select -select 'name CA and resid > 149 and resid < 211'
> >>>
> >>> should work.
> >>>
> >>>
> >>> It's a very powerful syntax and I figured for me it was very much
> >>> worth the effort reading through that documentation.
> >>>
> >> It's also simple in make_ndx:
> >>
> >> 3 & r 150-210
> >>
> >> Either way works. Whatever you find easier to use.
> >>
> >> -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
> >>
> >> ==
> >>
> >> --
> >> 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.
> >
> >
>
> --
> ==
>
> 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
>
> ==
>
> --
> 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.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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] Lipids running out of simulation box

[徐以会]

Dear all,

I am simulating a lipid bilayer under dehydration (1:5 lipid/water). In order 
to compare it with the bilayer periodicity d of X-ray diffraction. As the paper 
suggests for dehydrated membrane,
https://www.researchgate.net/publication/292341967_Solvent-exposed_lipid_tail_protrusions_depend_on_lipid_membrane_composition_and_curvature
I built up a double-bilayer using packmol rather than solvate (to precisely 
control the number of water).
As the water layer is very thin, many DOPC run out of the simulation box.  
Trjconv can surely repair the appearance, but I assume the bilayer periodicity 
(z1-z2) is longer accurate. 

So my questions:
(1) Is double bilayer a good system to obtain d?
(2) Does lipids out of box affect the calculation of d?
(3) If so, how to prevent it?  

Kind regards,
Yihui Xu
---
School of Physical Science and Technology at ShanghaiTech University
Shanghai, China

-- 
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] Index group for Backbone/C-alpha of specific stretch of residues

[Justin Lemkul]

On 1/9/20 9:42 AM, Navneet Kumar wrote:

Thank You, sir!

What If I want to extend the residues like choose c-alpha of 150-200 &
60-70 in a single index group ?


3 & r 60-70 | 3 & r 150-200

Type "help" at the make_ndx prompt for examples of how to use the program.

-Justin



On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul  wrote:



On 1/8/20 4:49 AM, Christian Blau wrote:

Hi Navnett,


gmx select will be your friend.


At the bottom of



http://manual.gromacs.org/documentation/current/onlinehelp/selections.html


you'll find some example commands. Something along the lines of

   gmx select -select 'name CA and resid > 149 and resid < 211'

should work.


It's a very powerful syntax and I figured for me it was very much
worth the effort reading through that documentation.


It's also simple in make_ndx:

3 & r 150-210

Either way works. Whatever you find easier to use.

-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

==

--
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.





--
==

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

==

--
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] CfP EuroVis 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

[Björn Sommer]

*Workshop on Molecular Graphics and Visual Analysis of Molecular Data *

*

(co-located with EuroVis & Eurographics 2020)

May 25th, 2020, Norrköping, Sweden



 

Molecular visualization and graphics is one of the oldest branches of
scientific visualization, which has been developing for over 50 years.
Due to the continuous advances in both computational biology and
computer graphics techniques, molecular graphics and visualization are
very active areas of research. Not only the ever-increasing dataset
sizes yield a constant challenge for visual analysis, but also new
technologies like advances in web-based graphics or augmented and
virtual reality open new possibilities. This half-day multidisciplinary
workshop - which is held in conjunction with EuroVis for the third time
and with Eurographics for the first time - brings together visualization
and computer graphics researchers working with molecular data.


Whereas molecular graphics is an established topic for many years, the
hybrid-dimensional visual analysis of molecular structures is still a
quite new research field with a lot of potential. We would like to
encourage submissions especially using new technologies, such as
immersive analytics or ML-related approaches.


We invite short papers as well as full papers (2-4 pages for short and
up to 8 pages for full papers, both with an additional page reserved for
references). All papers will undergo a single-stage, double-blind peer
review process. Accepted papers will be published in the EG digital
library. The workshop will be held in Norrköping, Sweden, May 25th,
2020, as part of EuroVis & Eurographics 2020.

  

Suggested topics include, but are not limited to:

- Molecular Graphics & Rendering

- Web-based Molecular Graphics & Visualization

- Immersive Analytics approaches using, e.g., VR/AR technologies

- Visual Analysis of Molecular Data (e.g., molecular structures,
biological networks, and pathways, or omics data)

- Visualization of Dynamic Molecular Data & Large Molecular Systems

- Tools papers describing new molecular visualization tools or novel
features in existing tools 

 

More info:

https://tinyurl.com/molva

 

Important Dates



Paper Submission Deadline:February 21, 2020

Notification of Acceptance:March 24, 2020

Camera-ready Deadline:April 8, 2020

Workshop Date:May 25, 2020

 

Organizers and Contact



- Jan Byska, University of Bergen, Norway

- Michael Krone, University of Tübingen, Germany

- Bjorn Sommer, Royal College of Art, UK

 

If you have any questions, please contact us:

mailto: molva.euro...@gmail.com  

 

Submission



Please submit your short and full papers via PCS (Deadline: February 21,
2020):

https://new.precisionconference.com/(EuroVis & Eurographics 2020 MolVA
Workshop)  


Please follow the EG guidelines for writing the paper. You can find more
info here and templates below:

https://www.eurovis.org/submission-guidelines/

https://tinyurl.com/MolVA2020-zip 


Best regards,

   Jan Byška, Michael Krone, Bjorn Sommer

   MolVA 2020 Organizing Committee

*
 
-- 
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 - Ryzen Architecture

[Szilárd Páll]

Good catch Kevin, that is likely an issue -- at least part of it.

Note that you can also use the mdrun -multidir functionality to avoid
having to manually manage mdrun process placement and pinning.

Another aspect is that if you leave half of the CPU cores unused, the cores
in use can boost to a higher clock rate and therefore can complete the work
on the CPU quicker which, as part of this work does not overlap with the
GPU, will impact the fraction of the time the GPU will be idle (and hence
also the time the GPU will be busy). For a fair comparison, run something
on those otherwise idle cores (at least a "stress -c 8" or possibly a
CPU-only mdrun); generally this is how we evaluate performance as a
function of CPU cores per GPU).

Cheers,
--
Szilárd


On Sat, Jan 4, 2020 at 9:11 PM Kevin Boyd  wrote:

> Hi,
>
> A few things besides any Ryzen-specific issues. First, your pinoffset for
> the second one should be 16, not 17. The way yours is set up, you're
> running on cores 0-15, then Gromacs will detect that your second
> simulation parameters are invalid (because from cores 17-32, core 32 does
> not exist) and turn off core pinning. You can verify that in the log file.
>
> Second, 16 threads per simulation is overkill, and you can get gains from
> stealing from GPU down-time by running 2 simulations per GPU. So I would
> suggest something like
>
> mdrun -nt 8 -pin on -pinoffset 0 -gpu_id 0 &
> mdrun -nt 8 -pin on -pinoffset 8 -gpu_id 0 &
> mdrun -nt 8 -pin on -pinoffset 16 -gpu_id 1 &
> mdrun -nt 8 -pin on -pinoffset 24 -gpu_id 1
>
> might give you close to optimal performance.
>
> On Thu, Jan 2, 2020 at 5:32 AM Paul bauer  wrote:
>
> > Hello,
> >
> > we only added full detection and support for the newer Rizen chip-sets
> > with GROMACS 2019.5, so please try if the update to this version solves
> > your issue.
> > If not, please open an issue on redmine.gromacs.org so we can track the
> > problem and try to solve it.
> >
> > Cheers
> >
> > Paul
> >
> > On 02/01/2020 13:26, Sandro Wrzalek wrote:
> > > Hi,
> > >
> > > happy new year!
> > >
> > > Now to my problem:
> > >
> > > I use Gromacs 2019.3 and to try to run some simulations (roughly 30k
> > > atoms per system) on my PC which has the following configuration:
> > >
> > > CPU: Ryzen 3950X (overclocked to 4.1 GHz)
> > >
> > > GPU #1: Nvidia RTX 2080 Ti
> > >
> > > GPU #2: Nvidia RTX 2080 Ti
> > >
> > > RAM: 64 GB
> > >
> > > PSU: 1600 Watts
> > >
> > >
> > > Each run uses one GPU and 16 of 32 logical cores. Doing only one run
> > > at time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU
> > > utilization is roughly around 84% but if I add a second run, the
> > > utilization of both GPUs drops to roughly 20%, while leaving logical
> > > cores 17-32 idle (I changed parameter gpu_id, accordingly).
> > >
> > > Adding additional parameters for each run:
> > >
> > > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu
> > > -pme gpu
> > >
> > > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu
> > > -pme gpu
> > >
> > > I get a utilization of 78% per GPU, which is nice but not near the 84%
> > > I got with only one run. In theory, however, it should come at least
> > > close to that utilization.
> > >
> > > I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems
> > > to prefer the the first Chiplet, even if two simultaneous simulations
> > > have the resources to occupy both. The reason for the 78% utilization
> > > could be because of overhead between the two Chiplets via the infinity
> > > band. However, I have no proof, nor am I able to explain why gmx mdrun
> > > -deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well -
> > > seems to occupy free logical cores then.
> > >
> > > Long story short:
> > >
> > > Are there any workarounds to squeeze the last bit out of my setup? Is
> > > it possible to choose the logical cores manually (I did not found
> > > anything in the docs so far)?
> > >
> > >
> > > Thank you for your help!
> > >
> > >
> > > Best,
> > >
> > > Sandro
> > >
> >
> > --
> > 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.
> >
> --
> 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 

Re: [gmx-users] is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version?

[Szilárd Páll]

On Wed, Jan 8, 2020 at 5:00 PM Jimmy Chen  wrote:

> Hi,
>
> is GPU peer access(RDMA) supported with inter-node and gmx2020 mpi version
> on NVidia GPU?
>

No, that is currently not implemented.

Cheers,
--
Szilárd

or just work only in single-node with threadMPI via Nvidia GPU direct?
>
> Thanks,
> Jimmy
> --
> 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] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thank You, sir!

What If I want to extend the residues like choose c-alpha of 150-200 &
60-70 in a single index group ?


On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul  wrote:

>
>
> On 1/8/20 4:49 AM, Christian Blau wrote:
> > Hi Navnett,
> >
> >
> > gmx select will be your friend.
> >
> >
> > At the bottom of
> >
> >
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >
> >
> > you'll find some example commands. Something along the lines of
> >
> >   gmx select -select 'name CA and resid > 149 and resid < 211'
> >
> > should work.
> >
> >
> > It's a very powerful syntax and I figured for me it was very much
> > worth the effort reading through that documentation.
> >
>
> It's also simple in make_ndx:
>
> 3 & r 150-210
>
> Either way works. Whatever you find easier to use.
>
> -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
>
> ==
>
> --
> 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.



-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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] Visualize replica exchange

[hind ahmed]

Dear All,

How can I visualize replica exchange in VMD?

Thanks
-- 
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] Replica exchange probabilities and extend simulation

[hind ahmed]

Dear All,

 Are these probabilities good? and how can I extend the simulation of 
replica-exchange?

Thanks

Replica exchange statistics
Repl  14999 attempts, 7500 odd, 7499 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  
.01  .01  .01  .01  .01  .01  .01  .01  .02  .02  .02  .01  .02  .02  .02  .02  
.02
Repl  number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  259  263  270  330   62   57   63   58   65   67   71   74   89   87  
 88  103  100  103   98   98  114   93  132  127  149  111  117  126  129  124  
145
Repl  average number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31
Repl  .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  
.01  .01  .01  .01  .01  .01  .02  .01  .02  .02  .02  .01  .02  .02  .02  .02  
.02

-- 
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] charting Ligand's movement in the binding pocket

[Prasanth G, Research Scholar]

Dear All,

I am interested in charting the trajectory of the ligand with respect to
the residues of the binding pocket, during the simulation.
May be representing the center of mass of the ligand as a dot at each
frame, would help us see the path traced by the ligand in the pocket,
during the simulation. Is there a possibility to do this during the
trajectory analysis period / post production..?
I was wondering if we could perform PCA and impose the ligand's trajectory
on the bound complex and visualize only the ligand's movement with respect
to the amino acid residues of the binding pocket. But this would not give a
clear idea as the residues in binding pocket also move during the course of
simulation.
Hoping that i was able to explain it well enough..
Thank you in advance.

-- 
Regards,
Prasanth.
-- 
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.