Re: [gmx-users] Tetrahedral order
On 7/9/19 4:24 AM, Omkar Singh wrote: Dear all, I want to calculate the Tetrahedral order parameter through gmx. Can anyone help? Eventhough I tried but my system has 500 water molecules Fir that I am unable to make index file because it will take lots of time for typing any suggestions. Commend gmx order -f .xtc -s .tpr -b 0 -e 1 -n .ndx -nr .ndx -d y -permolecule You're using the wrong tool. gmx order is explicitly for carbon atoms, e.g. alkyl chains in phospholipids. You want gmx hydorder. -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.
Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb
On 7/9/19 2:59 AM, Carlos Navarro wrote: Dear Justin, Thanks for the reply. I forgot to mention that indeed the reason of using Berger lipids is because there are united-atom. I'm planning on running computational electrophysiology simulations, and since my system is about 600k atoms I want to use vsites, as De Groot has been doing recently https://www.nature.com/articles/s41467-018-03179-y The only source of parameters and coordinates that I know of: http://wcm.ucalgary.ca/tieleman/downloads -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.
[gmx-users] make test failed during installing gromacs
Hello, everyone, When I run make test during installing gromacs-2019.3 in centos 7 in a workstation with 4 Tesla 1080 GPU, I get the following failure information: The following tests FAILED: 10 - GpuUtilsUnitTests (Timeout) 38 - MdrunNonIntegratorTests (Timeout) 42 - regressiontests/complex (Failed) Errors while running CTest make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 make[1]: *** [CMakeFiles/check.dir/rule] Error 2 make: *** [check] Error 2 Will the installation finally failed? Should I continue to run "make install"? Best regards -- 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] Install on Windows 10 with AMD GPU
Thanks Szilárd,
No difference unfortunately. I wonder if it is due to the new headers files
that are no longer version specific.
I will see if I can track down an old version
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Szilárd Páll
Sent: Tuesday, 9 July 2019 10:46 PM
To: Discussion list for GROMACS users
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Install on Windows 10 with AMD GPU
Hi James,
On Mon, Jul 8, 2019 at 10:57 AM James Burchfield <
james.burchfi...@sydney.edu.au> wrote:
> Thankyou Szilárd,
> Headers are available here
> https://protect-au.mimecast.com/s/-oPwCNLwM9ixRV85smybKT?domain=github
> .com
> But I get
> CMake Error at cmake/gmxManageOpenCL.cmake:45 (message):
> OpenCL is not supported. OpenCL version 1.2 or newer is required.
> Call Stack (most recent call first):
> CMakeLists.txt:236 (include)
>
> I am setting
> OpenCL_include_DIR to C:/Users/Admin/ OpenCL-Headers-master/CL
>
That path should not include "CL" (the header is expected to be included as
CL/cl.h).
Let me know if that helps.
--
Szilárd
> OpenCL_INCLUDE_DIR OpenCL_Library to C:/Windows/System32/OpenCL.dll
>
>
> The error file includes
> Microsoft (R) C/C++ Optimizing Compiler Version 19.21.27702.2 for
> x64
>
> CheckSymbolExists.c
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
> cl /c /Zi /W3 /WX- /diagnostics:column /Od /Ob0 /D WIN32 /D _WINDOWS
> /D "CMAKE_INTDIR=\"Debug\"" /D _MBCS /Gm- /RTC1 /MDd /GS /fp:precise
> /Zc:wchar_t /Zc:forScope /Zc:inline /Fo"cmTC_2c430.dir\Debug\\"
> /Fd"cmTC_2c430.dir\Debug\vc142.pdb" /Gd /TC /errorReport:queue
> "C:\Program Files\gromacs\CMakeFiles\CMakeTmp\CheckSymbolExists.c"
>
> C:\Program Files\gromacs\CMakeFiles\CMakeTmp\CheckSymbolExists.c(2,10):
> error C1083: Cannot open include file:
> 'OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h': No such file or directory
> [C:\Program Files\gromacs\CMakeFiles\CMakeTmp\cmTC_2c430.vcxproj]
>
>
> File C:/Program Files/gromacs/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include
>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef CL_VERSION_1_0
> return ((int*)(_VERSION_1_0))[argc]; #else
> (void)argc;
> return 0;
> #endif
> }
>
>
> Guessing it is time to give up
>
> Cheers
> James
>
>
>
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Szilárd
> Páll
> Sent: Friday, 5 July 2019 10:20 PM
> To: Discussion list for GROMACS users
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Install on Windows 10 with AMD GPU
>
> Dear James,
>
> Unfortunately, we have very little experience with OpenCL on Windows, so I
> am afraid I can not advise you on specifics. However, note that the only
> part of the former SDK that is needed is the OpenCL headers and loader
> libraries (libOpenCL) which is open source software that can be obtained
> from the standards body, KHronos. Not sure what the mechanism is for
> Windows, but for Linux these components are in packaged in the standard
> repositories of most distributions.
>
> However, before going through a large effort of trying to get GROMACS
> running on Windows + AMD + OpenCL, you might want to consider evaluating
> the potential benefits of the hardware. As these cards are quite dated you
> might find that they do not provide enough performance benefit to warrant
> the effort required -- especially as, if you have a workstation with
> significant CPU resources, you might find that GROMACS runs nearly as fast
> or faster on the CPU only (that's because we have very efficient CPU SIMD
> code for all compute-intensive work).
>
> To do a hopefully easier quick performance evaluation, you could simply
> boot a Linux distribution off of an external disk, you can find Linux
> drivers for them for Ubuntu 16.04/18.04 at least which you can install and
> see how well does the system perform.
>
> I hope that helps!
>
> Cheers,
> --
> Szilárd
>
>
> On Fri, Jul 5, 2019 at 9:11 AM James Burchfield <
> james.burchfi...@sydney.edu.au> wrote:
>
> > Hi there,
> >
> > I was hoping to install gromacs on a windows10 system that runs 2 AMD
> > Firepro cards.
> > I have managed to achieve almost everything in terms of setting up the
> > compilation with the exception of OpenCl.
> >
> > The issue I have run into are in reference to the settings of
> >
> > CMAKE_PREFIX_PATH (unsure if I need to put anything here)
> > OpenCL_INCLUDE_DIR OpenCL_Library
> >
> > The cards I am running are~ 5years old Firepro W7100 OpenCL version
> > they are running is 2.0
> >
> >
> > AMD no longer makes the OpenCL SDK
> > Apparrently, most of the relevant stuff is now included with the
> > drivers and headers can be downloaded from GitHub
> >
> > I have tried
> >
> > * Installing the old SDK
> > * Installing the newer "light" version of the SDK
> > * Downloading
[gmx-users] rtx 2080 gpu
Dear all, I have a centOS machine equipped with two RTX 2080 cards, with nvidia drivers 430.2; I installed cuda toolkit 10-1. when executing mdrun the log reported the following message: GROMACS version:2019.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: NONE FFT library:fftw-3.3.8 RDTSCP usage: disabled TNG support:enabled Hwloc support: disabled Tracing support:disabled C compiler: /usr/bin/cc GNU 4.8.5 C compiler flags:-O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 4.8.5 C++ compiler flags: -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, V10.1.168 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;; ;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver:10.20 CUDA runtime: N/A NOTE: Detection of GPUs failed. The API reported: unknown error GROMACS cannot run tasks on a GPU. Does anyone have any suggestions? Thanks in advance Stefano -- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178 -- 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] Self-interaction across periodic boundaries
Possibly turn pbc off and use nvt PB > On Jul 8, 2019, at 1:31 PM, Salman Zarrini wrote: > > Thanks Mark. > The problem is that I would like to keep the overall concentration > constant, so, using a larger box e.g. with 2 times larger lateral box > dimensions, > needs me to increase the number of molecules 8 times, so even more likely > to lead to percolating structures in a larger simulation box. > > Best regards, > Salman Zarrini > > On Mon, Jul 8, 2019 at 6:24 AM Mark Abraham > wrote: > >> Hi, >> >> If you're trying to model something like it was at infinite dilution using >> a periodic box, then the size of the box needs to be at least as large as >> the size of the structure and its effective interaction radius. It seems >> like your simulation is suggesting at least one of those is larger than you >> first thought it was :-) >> >> Mark >> >> On Mon, 8 Jul 2019 at 11:58, Salman Zarrini >> wrote: >> >>> Dear all, >>> Using MD simulations I expect to observe aggregation among some molecules >>> solvated in water to have ultimately a droplet out of the molecules. The >>> aggregates form to some extent in the course of simulation time, however, >>> after a while the system become kinetically trapped in artificial >>> percolating aggregates in which the molecules are self-interacting across >>> the periodic boundaries. >>> I wonder if there is any possibility to prevent aggregates >> self-interaction >>> across periodic boundaries? >>> >>> Thank you, >>> Salman >>> -- >>> Best regards, >>> >>> Salman Zarrini >>> -- >>> 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 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.
[gmx-users] questions about Ryckaert-Bellemans type dihedrals
Hi, I have a question regarding Ryckaert-Bellemans dihedral potentials (function type 3). In the manual of GROMACS 4.5.4 it says to use Ryckaert-Bellemans type, one needs to erase the 1-4 interaction in [pairs] section. My first question is what will happen if I use this potential (type 3) but leave the 1-4 interaction in [pairs] section? Next in the newer version GROMACS (5.1.4) the manual says: *In the original implementation of the potential for alkanes no 1-4 interactions were used, which means that in order to implement that particular force field you need to remove the 1-4 interactions from the [ pairs ] section of your topology. In most modern force fields, like OPLS/AA or Amber the rules are different, and the Ryckaert-Bellemans potential is used as a cosine series in combination with 1-4 interactions.* What force field is considered as most modern force fields? (I'm using AMBER ff99SB-ildn-nmr.) Again what will happen if I don't remove those 1-4 interactions in the [pairs] section? My last question is should I expect huge differences between Ryckaert-Bllemans potential (type 3) and periodic (type 9) in simulations of the same molecule? I plan to run some simulation to test that but I wonder if there is a general answer based on the previous experience. Based on the manual I know RB potential excludes 1-4 interactions whereas periodic type include 1-4 interactions. I'm not clear about the performance difference between these two dihedral types. Also if RB potential requires the exclusion of 1-4 interactions why the manual says in modern force fields it is used in combination with 1-4 interactions. I'm familiar about this part and I do hope to learn more about this. Thank you for your time in advance! Best, Yunhui 1. -- 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] How to let mdrun not generate trr file
Hi, If you set nstxout, nstvout and nstfount to zero, then the trr file will have no content. I'm not sure offhand whether that triggers omitting even opening the file... Mark On Tue, 9 Jul 2019 at 17:29, sunyeping wrote: > Hello everyone, > > "gmx mdrun -dffname md_0_1" will generate all production files including > .trr, .xtc, .cpt, .log, etc.. If I don't want it to generate .trr file but > generate all other file types, how should I write the command? > > Best regards > > Yeping Sun > -- > 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.
[gmx-users] How to let mdrun not generate trr file
Hello everyone, "gmx mdrun -dffname md_0_1" will generate all production files including .trr, .xtc, .cpt, .log, etc.. If I don't want it to generate .trr file but generate all other file types, how should I write the command? Best regards Yeping Sun -- 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 the maximum number of atoms that GROMACS can simulate?
Hi Zhang, > On 9. Jul 2019, at 15:16, 张驭洲 wrote: > > Hello， > > I want to know if there is a maximum number of atoms that GROMACS can > simulate, or if there are any bugs in the code that cause the error in > computing the coordinate of atoms when the number of atoms is very large? I'm > trying to simulate some very large systems using GROMACS-2019.3. > Unfortunately, the energy minimization crashed during the run. I tried using > more than one compute nodes, for example, 4, 8 or 32, and I'm sure the memory > is not exhausted. The system I tried contains more than 100 million atoms. There is no limit on the number of atoms that you can simulate in GROMACS. However, if the simulation systems become very large in at least one dimension, you might need double precision, as single precision could be insufficient to accurately store the positions of atoms that are far off the origin. This can then lead to a positive energy drift which could become so large that the system gets instable. A while time ago we have observed such problems with large systems of mostly vacuum, which contained several water droplets. The droplets that were farthest away from the origin would start to heat up and eventually evaporate after some time, unless a double precision version of mdrun was used. Carsten > > Zhang > -- > 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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 the maximum number of atoms that GROMACS can simulate?
Hello， I want to know if there is a maximum number of atoms that GROMACS can simulate, or if there are any bugs in the code that cause the error in computing the coordinate of atoms when the number of atoms is very large? I'm trying to simulate some very large systems using GROMACS-2019.3. Unfortunately, the energy minimization crashed during the run. I tried using more than one compute nodes, for example, 4, 8 or 32, and I'm sure the memory is not exhausted. The system I tried contains more than 100 million atoms. Zhang -- 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] Install on Windows 10 with AMD GPU
Hi James,
On Mon, Jul 8, 2019 at 10:57 AM James Burchfield <
james.burchfi...@sydney.edu.au> wrote:
> Thankyou Szilárd,
> Headers are available here https://github.com/KhronosGroup/OpenCL-Headers
> But I get
> CMake Error at cmake/gmxManageOpenCL.cmake:45 (message):
> OpenCL is not supported. OpenCL version 1.2 or newer is required.
> Call Stack (most recent call first):
> CMakeLists.txt:236 (include)
>
> I am setting
> OpenCL_include_DIR to C:/Users/Admin/ OpenCL-Headers-master/CL
>
That path should not include "CL" (the header is expected to be included as
CL/cl.h).
Let me know if that helps.
--
Szilárd
> OpenCL_INCLUDE_DIR OpenCL_Library to C:/Windows/System32/OpenCL.dll
>
>
> The error file includes
> Microsoft (R) C/C++ Optimizing Compiler Version 19.21.27702.2 for x64
>
> CheckSymbolExists.c
>
> Copyright (C) Microsoft Corporation. All rights reserved.
>
> cl /c /Zi /W3 /WX- /diagnostics:column /Od /Ob0 /D WIN32 /D _WINDOWS /D
> "CMAKE_INTDIR=\"Debug\"" /D _MBCS /Gm- /RTC1 /MDd /GS /fp:precise
> /Zc:wchar_t /Zc:forScope /Zc:inline /Fo"cmTC_2c430.dir\Debug\\"
> /Fd"cmTC_2c430.dir\Debug\vc142.pdb" /Gd /TC /errorReport:queue "C:\Program
> Files\gromacs\CMakeFiles\CMakeTmp\CheckSymbolExists.c"
>
> C:\Program Files\gromacs\CMakeFiles\CMakeTmp\CheckSymbolExists.c(2,10):
> error C1083: Cannot open include file:
> 'OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h': No such file or directory
> [C:\Program Files\gromacs\CMakeFiles\CMakeTmp\cmTC_2c430.vcxproj]
>
>
> File C:/Program Files/gromacs/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include
>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef CL_VERSION_1_0
> return ((int*)(_VERSION_1_0))[argc];
> #else
> (void)argc;
> return 0;
> #endif
> }
>
>
> Guessing it is time to give up
>
> Cheers
> James
>
>
>
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Szilárd
> Páll
> Sent: Friday, 5 July 2019 10:20 PM
> To: Discussion list for GROMACS users
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Install on Windows 10 with AMD GPU
>
> Dear James,
>
> Unfortunately, we have very little experience with OpenCL on Windows, so I
> am afraid I can not advise you on specifics. However, note that the only
> part of the former SDK that is needed is the OpenCL headers and loader
> libraries (libOpenCL) which is open source software that can be obtained
> from the standards body, KHronos. Not sure what the mechanism is for
> Windows, but for Linux these components are in packaged in the standard
> repositories of most distributions.
>
> However, before going through a large effort of trying to get GROMACS
> running on Windows + AMD + OpenCL, you might want to consider evaluating
> the potential benefits of the hardware. As these cards are quite dated you
> might find that they do not provide enough performance benefit to warrant
> the effort required -- especially as, if you have a workstation with
> significant CPU resources, you might find that GROMACS runs nearly as fast
> or faster on the CPU only (that's because we have very efficient CPU SIMD
> code for all compute-intensive work).
>
> To do a hopefully easier quick performance evaluation, you could simply
> boot a Linux distribution off of an external disk, you can find Linux
> drivers for them for Ubuntu 16.04/18.04 at least which you can install and
> see how well does the system perform.
>
> I hope that helps!
>
> Cheers,
> --
> Szilárd
>
>
> On Fri, Jul 5, 2019 at 9:11 AM James Burchfield <
> james.burchfi...@sydney.edu.au> wrote:
>
> > Hi there,
> >
> > I was hoping to install gromacs on a windows10 system that runs 2 AMD
> > Firepro cards.
> > I have managed to achieve almost everything in terms of setting up the
> > compilation with the exception of OpenCl.
> >
> > The issue I have run into are in reference to the settings of
> >
> > CMAKE_PREFIX_PATH (unsure if I need to put anything here)
> > OpenCL_INCLUDE_DIR OpenCL_Library
> >
> > The cards I am running are~ 5years old Firepro W7100 OpenCL version
> > they are running is 2.0
> >
> >
> > AMD no longer makes the OpenCL SDK
> > Apparrently, most of the relevant stuff is now included with the
> > drivers and headers can be downloaded from GitHub
> >
> > I have tried
> >
> > * Installing the old SDK
> > * Installing the newer "light" version of the SDK
> > * Downloading the headers
> >
> > Whatever the case
> > I cannot get it to work .
> > I get an error saying that the minimum requirement is openCl 1.2.
> > According to the AMD driver the cards are running opencl 2.0
> >
> > Any help would be appreciated
> >
> > Cheers,
> > James
> >
> >
> >
> > Dr James Burchfield
> > Group Leader - Molecular Imaging
> > Metabolic Cybernetics Laboratory | School of Life and Environmental
> > Sciences
> > D17 - Charles Perkins Centre | The University of
[gmx-users] Tetrahedral order
Dear all, I want to calculate the Tetrahedral order parameter through gmx. Can anyone help? Eventhough I tried but my system has 500 water molecules Fir that I am unable to make index file because it will take lots of time for typing any suggestions. Commend gmx order -f .xtc -s .tpr -b 0 -e 1 -n .ndx -nr .ndx -d y -permolecule -- 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] POPC Berger lipids parameters for AMBER99sb
Dear Justin, To use a time step of 4fs(i clicked send by.mistake) On Tue, Jul 9, 2019 at 7:59 AM Carlos Navarro wrote: > Dear Justin, > Thanks for the reply. > I forgot to mention that indeed the reason of using Berger lipids is > because there are united-atom. I'm planning on running computational > electrophysiology simulations, and since my system is about 600k atoms I > want to use vsites, as De Groot has been doing recently > https://www.nature.com/articles/s41467-018-03179-y > Best regards, > Carlos > > On Tue, Jul 9, 2019 at 1:50 AM Justin Lemkul wrote: > >> >> >> On 7/8/19 7:31 PM, Carlos Navarro wrote: >> > Dear gmx-users, >> > I was wondering if someone can share the Berger parameters for POPC for >> > Amber99sb (and I they can share also a .pdb .gro file will be even >> better). >> > I found several for gromos, but I need them form AMBER99sb. >> >> Berger parameters are united-atom and designed for use with GROMOS. I >> know some people have combined them with various protein force fields >> with varying success, but I would not do that. Berger parameters are >> wildly outdated and much better force fields exist. In your case, use >> Slipids, which are specifically designed to be compatible with AMBER. >> >> -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. >> > -- > > -- > > Carlos Navarro Retamal > > Bioinformatic Engineering. PhD > > Postdoctoral Researcher in Center for Bioinformatics and Molecular > Simulations > > Universidad de Talca > > Av. Lircay S/N, Talca, Chile > > T: (+56) 712201 798 > > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > -- -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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] POPC Berger lipids parameters for AMBER99sb
Dear Justin, Thanks for the reply. I forgot to mention that indeed the reason of using Berger lipids is because there are united-atom. I'm planning on running computational electrophysiology simulations, and since my system is about 600k atoms I want to use vsites, as De Groot has been doing recently https://www.nature.com/articles/s41467-018-03179-y Best regards, Carlos On Tue, Jul 9, 2019 at 1:50 AM Justin Lemkul wrote: > > > On 7/8/19 7:31 PM, Carlos Navarro wrote: > > Dear gmx-users, > > I was wondering if someone can share the Berger parameters for POPC for > > Amber99sb (and I they can share also a .pdb .gro file will be even > better). > > I found several for gromos, but I need them form AMBER99sb. > > Berger parameters are united-atom and designed for use with GROMOS. I > know some people have combined them with various protein force fields > with varying success, but I would not do that. Berger parameters are > wildly outdated and much better force fields exist. In your case, use > Slipids, which are specifically designed to be compatible with AMBER. > > -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. > -- -- Carlos Navarro Retamal Bioinformatic Engineering. PhD Postdoctoral Researcher in Center for Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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.
