[gmx-users] QMMM with GROMACS and DFTB3

[S M Bargeen Turzo]

Hello everyone,

I was wondering if GROMACS 2016(or 2018) can be interfaced with any QM
program like GAMESS-US or ORCA.
So far from my searches I found out that it can be done using GROMACS
version 5 and DFTB3 according to this website:
http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3

However the official gromacs website does not mention anything about DFTB3
or ORCA, so I need some guidance here regarding which version of GROMACS
should I be compiling with which QM program.


Thanks
-Bargeen
-- 
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] cudaMallocHost filed: unknown error

[Szilárd Páll]

As a side-note, your mdrun invocation does not seem suitable for GPU
accelerated runs, you'd most likely be better of running fewer ranks.
--
Szilárd


On Fri, Mar 23, 2018 at 9:26 PM, Christopher Neale
 wrote:
> Hello,
>
> I am running gromacs 5.1.2 on single nodes where the run is set to use 32 
> cores and 4 GPUs. The run command is:
>
> mpirun -np 32 gmx_mpi mdrun -deffnm MD -maxh $maxh -dd 4 4 2 -npme 0 -gpu_id 
>  -ntomp 1 -notunepme
>
> Some of my runs die with this error:
> cudaMallocHost of size 1024128 bytes failed: unknown error
>
> Below is the relevant part of the .log file. Searching the internet didn't 
> turn up any solutions. I'll contact sysadmins if you think this is likely 
> some problem with the hardware or rogue jobs. In my testing, a collection of 
> 24 jobs had 6 die with this same error message (including the "1024128 bytes" 
> and "pmalloc_cuda.cu, line: 70"). All on different nodes, and all those node 
> next took repeat jobs that run fine. When the error occured, it was always 
> right at the start of the run.
>
>
> Thank you for your help,
> Chris.
>
>
>
> Command line:
>   gmx_mpi mdrun -deffnm MD -maxh 0.9 -dd 4 4 2 -npme 0 -gpu_id 
>  -ntomp 1 -notunepme
>
>
> Number of logical cores detected (72) does not match the number reported by 
> OpenMP (2).
> Consider setting the launch configuration manually!
>
> Running on 1 node with total 36 cores, 72 logical cores, 4 compatible GPUs
> Hardware detected on host ko026.localdomain (the node of MPI rank 0):
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Xeon(R) CPU E5-2695 v4 @ 2.10GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: AVX2_256
>   GPU info:
> Number of GPUs detected: 4
> #0: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: 
> compatible
> #1: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: 
> compatible
> #2: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: 
> compatible
> #3: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: 
> compatible
>
> Reading file MD.tpr, VERSION 5.1.2 (single precision)
> Can not increase nstlist because verlet-buffer-tolerance is not set or used
> Using 32 MPI processes
> Using 1 OpenMP thread per MPI process
>
> On host ko026.localdomain 4 GPUs user-selected for this run.
> Mapping of GPU IDs to the 32 PP ranks in this node: 
> 0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3
>
> NOTE: You assigned GPUs to multiple MPI processes.
>
> NOTE: Your choice of number of MPI ranks and amount of resources results in 
> using 1 OpenMP threads per rank, which is most likely inefficient. The 
> optimum is usually between 2 and 6 threads per rank.
>
>
> NOTE: GROMACS was configured without NVML support hence it can not exploit
>   application clocks of the detected Tesla P100-PCIE-16GB GPU to improve 
> performance.
>   Recompile with the NVML library (compatible with the driver used) or 
> set application clocks manually.
>
>
> ---
> Program gmx mdrun, VERSION 5.1.2
> Source code file: 
> /net/scratch3/cneale/exe/KODIAK/GROMACS/source/gromacs-5.1.2/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu,
>  line: 70
>
> Fatal error:
> cudaMallocHost of size 1024128 bytes failed: unknown error
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Halting parallel program gmx mdrun on rank 31 out of 32
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31
>
>
> --
> 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] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??

[Szilárd Páll]

rlist >= rcoulomb / rvdw is the correct one, the list cutoff has to be
at least as long as the longest of the interaction cut-offs.
--
Szilárd


On Mon, Mar 26, 2018 at 1:05 PM, huolei peng  wrote:
> In the user guide of Gromacs 2016 (or 2018), it shows " rlist>=rcoulomb "
>  or "rlist>=rvdw" in several places (see the links below), which are in
> contrast to those in version of 5.15.  Are those changes due to typos?
> Thanks.
>
>
> http://manual.gromacs.org/documentation/2016-current/user-guide/mdp-options.html
>
> http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html
>
> http://manual.gromacs.org/documentation/5.1-current/user-guide/mdp-options.html
>
>
>
> Best,
>
> Peng
> --
> 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] What's new in GROMACS 2018? - a BioExcel webinar

[Rossen Apostolov]

Hi again,

We just realized there was a mistake on the website, and the *webinar is 
scheduled for 13:00 BST (UK) / 14:00 CEST time.*


The GoToWebinar platform, where you register, has the correct time.

Rossen


On 2018-03-26 11:25, Rossen Apostolov wrote:


Dear GROMACS users,

BioExcel CoE (https://bioexcel.eu) is organizing *tomorrow from 14:00 
GMT (15:00 CEST) *a webinar on the features, hardware support and 
various enhancements in the latest 2018 major release. At the end of 
the presentation, Mark Abraham, the GROMACS development manager, will 
answer your questions regarding the release.


You can register here: 
https://bioexcel.eu/webinar-gromacs-2018-overview-of-the-new-features-and-capabilities-2018-03-27/


Note that we have a limit of 100 attendees and there are already over 
50 registrants.


Rossen



--
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] why "gmx gyrate" could not be supplied with "-tu ns" option?

[Justin Lemkul]

On 3/26/18 8:01 AM, ZHANG Cheng wrote:

Dear Gromacs,
I use Command line:


   gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns



and was told:


Error in user input:
Invalid command-line options
 Unknown command-line option -tu



So why "gyrate" could not be supplied with "-tu ns" option?


Not all analysis programs have that option.

-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.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] why "gmx gyrate" could not be supplied with "-tu ns" option?

[ZHANG Cheng]

Dear Gromacs,
I use Command line:


  gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns



and was told:


Error in user input:
Invalid command-line options
Unknown command-line option -tu



So why "gyrate" could not be supplied with "-tu ns" option?


Thank you.


Yours sincerely
Cheng
-- 
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] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??

[huolei peng]

In the user guide of Gromacs 2016 (or 2018), it shows " rlist>=rcoulomb "
 or "rlist>=rvdw" in several places (see the links below), which are in
contrast to those in version of 5.15.  Are those changes due to typos?
Thanks.


http://manual.gromacs.org/documentation/2016-current/user-guide/mdp-options.html

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html

http://manual.gromacs.org/documentation/5.1-current/user-guide/mdp-options.html



Best,

Peng
-- 
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] Periodicity in umbrella sampling

[Matteo Busato]

Hi to everyone,


I am performing an umbrella sampling simulation of an ion pulled through a 
biphasic system. The box is 3.6 X 3.6 X 7.3 nm and the ion has been pulled 
along the z-axys for about 3 nm.


In Justin Lemkul's tutorial about umbrella sampling 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/02_define_box.html)
 I've read that "one must allow enough space in the pulling direction to allow 
for a continuous pull without interacting with the periodic images of the 
system".

This turns into the fact that the pulling distance must always be less than 
half the box size in the pulling direction, but what about the other two 
directions? In my case, if I put no restraints on the x and y-axes movements of 
my ion, it will probably interact with the periodic images of the box in the x 
and y directions (e.g. go out from a box surface and get in by the other side).

Could this affect the final PMF result?


Thank you in advance for your answer.


Regards,

Matteo
-- 
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] What's new in GROMACS 2018? - a BioExcel webinar

[Rossen Apostolov]

Dear GROMACS users,

BioExcel CoE (https://bioexcel.eu) is organizing *tomorrow from 14:00 
GMT (15:00 CEST) *a webinar on the features, hardware support and 
various enhancements in the latest 2018 major release. At the end of the 
presentation, Mark Abraham, the GROMACS development manager, will answer 
your questions regarding the release.


You can register here: 
https://bioexcel.eu/webinar-gromacs-2018-overview-of-the-new-features-and-capabilities-2018-03-27/


Note that we have a limit of 100 attendees and there are already over 50 
registrants.


Rossen

--
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.