Re: [gmx-users] Free energy calculation of Histone
Hi, That's the wrong way around. :-) One doesn't do a lab experiment first and then decide what you wanted to observe from it, to either :-). There are tutorials for computing free energy of solvation, which I suggest you follow, and I suspect your fully solvated simulation won't be useful for that. Mark On Thu., 10 Jan. 2019, 02:45 Ayesha Kanwal, wrote: > Dear all users, > I am new for using GROMACS. and also read the tutorial of Methane and > water. I have already simulated data of 100 ns for four histones. I want to > know how to calculate free energy solvation from this data. which topology > file and coordinate files I will use? > I will appreciate your good suggestions. > > Regards > Ayesha > > -- > 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] calculate interaction energy between two proteins
thank you so much. now i understand this. On 1/9/19, Justin Lemkul wrote: > > > On 1/9/19 3:31 AM, SHAHEE ISLAM wrote: >> it is connected with aggregation phenomenon. > > Maybe, but no force field is parametrized with protein aggregation in > mind. Mark is cautioning you that you may be seeking a meaningless > quantity. > > To calculate the interaction energy, you need to define energygrps in > your .mdp file (each protein in a separate group), generate a new .tpr > file, then use mdrun -rerun to re-evaluate the energies with these > groups from the existing trajectory. Then it is your job to convince > your skeptical audience that such a quantity actually means anything. > > -Justin > >> On 1/9/19, Mark Abraham wrote: >>> Hi, >>> >>> How is the protein-protein interaction energy defined? What physical >>> observable is it connected to? >>> >>> Mark >>> >>> On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM >>> wrote: >>> can anyone please tell me, if i select 42 then wheather it will calculate the protein-protein interaction energy? because i did not define two proteins in the mdp file.i just mentioned protein.I am not understanding this. thanking you On 1/8/19, SHAHEE ISLAM wrote: > hi, > i want to calculate interaction energy between two protein. > In my system there are two proteins,waters and ions.In my .mdp file > the, energygrps = PROTEIN W ION > i am using this command > gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg > then the following options are coming > > 1 Bond 2 G96Angle 3 Proper-Dih. 4 > Improper-Dih. >5 LJ-(SR) 6 Coulomb-(SR) 7 Potential8 > Kinetic-En. >9 Total-Energy10 Temperature 11 Pressure12 > Constr.-rmsd > 13 Box-X 14 Box-Y 15 Box-Z 16 > Volume > 17 Density 18 pV 19 Enthalpy20 > Vir-XX > 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 > Vir-YY > 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 > Vir-ZZ > 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 > Pres-YX > 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 > Pres-ZY > 37 Pres-ZZ 38 #Surf*SurfTen 39 Box-Vel-XX 40 Box-Vel-YY > 41 Box-Vel-ZZ 42 Coul-SR:Protein-Protein > 43 LJ-SR:Protein-Protein 44 Coul-SR:Protein-W > 45 LJ-SR:Protein-W 46 Coul-SR:Protein-ION > 47 LJ-SR:Protein-ION 48 Coul-SR:W-W > 49 LJ-SR:W-W 50 Coul-SR:W-ION > 51 LJ-SR:W-ION 52 Coul-SR:ION-ION > 53 LJ-SR:ION-ION 54 T-Protein 55 T-W 56 > T-ION > 57 Lamb-Protein58 Lamb-W 59 Lamb-ION > > if i select 42 and 43. will it give me the total energy value > considering both proteins. > or what should i correctly select. > thanking you > Shahee Islam > -- 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. >>> > > -- > == > > 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. > -- 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 vi
Re: [gmx-users] Dihedral restraints
Hi, You can see a working example at https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log so I conclude that your restraints are inactive, somehow. Please check your include statements, etc. Mark On Wed., 9 Jan. 2019, 18:05 ABEL Stephane, wrote: > Thanks Mark for your reply > > In the log and edr files I only see an "Position Rest." term. So do you > mean that the contributions on the dihedral restrains is added in in total > energy without additional terms in the energy output in log file and the > edr ? > > Thank you in advance for the clarification. > > Stéphane > > > -- > > Message: 3 > Date: Wed, 9 Jan 2019 12:32:31 +0100 > From: Mark Abraham > To: gmx-us...@gromacs.org > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] Dihedral restraints > Message-ID: > xv8qbic+t1h1cwwcnkisdfxnoja7xbot...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > IIRC that's enough, for dihedral restraints. You will see energy > contributions from the the restraints appear in your .log and .edr files if > the restraints are active. I don't recall if there is anything printed by > mdrun before the simulation commences. > > Mark > > On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane > wrote: > > > Hello > > > > I would like to apply some dihedral restraints in different residues of > my > > protein during the production stage. For that I have added at the end of > > the protein itp the section > > [ dihedral_restraints ]. Is it enough ? Should I add something else in > the > > mdp ? In other words, how to be sure that the restraints are effectively > > applied during the run ? > > > > I am using GROMACS 2018.2 > > > > Thank in advance and happy new year to all > > > > St?phane > > -- > -- > 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] Free energy calculation of Histone
Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate your good suggestions. Regards Ayesha -- 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] AMD 32 core TR
Tomas, Again, thanks for the response. On re-reading the data Exxact Corp sent ( always helps to review) they did use a 2080ti and two zions. Your point on maxing out the GPU is interesting. On the 8 core ( 16T) the GPU is maxed out as you inferred, but not on the 32 core (64T) with which the GPU runs at 60-85% depending on the model but still at greater efficiency than the 8 core ( ~ 60 vs 50 ns/day. I’ve never been able to max out the GTX 1080 TI on the 32 core system. The primary reason for the 32 core is to support two GPUs and there the efficiency increases from (e.g ) 70 ns/day to 90 -100 ns/day with ~ 150k atoms. I never expected a tremendous increase by increasing core number I feel a little uncomfortable citing such generalities. So for now I will state that am satisfied with the outcome and that users who use single workstations can expect to match professionally assembled systems. > On Jan 6, 2019, at 5:07 AM, Tamas Hegedus wrote: > > It also comes into my mind that the AMD 32 core has not a double performance > of AMD 16 core. Because of manufacturing the 4 dies (4x8 cpu units), it does > not have the same bandwidth to the RAM. But this is told to affect only > memory hungry applications. Thus at this moment I think that this does not > effect much gmx runs. I hope to try an RT 2990WX (amd 32core) in 1-2 months. > > On 2019. 01. 04. 4:18, paul buscemi wrote: >> Tamas, thanks for the response. >> In previous posts I mention using a single gtx 1080ti, sorry for not making >> it clear in the last post. >>On the 8 core AMD and an Intel 6 core I am running Cuda 10 with Gromacs >> 18.3 with no issues. I believe the larger factor in the slowness of the 32 >> core was in having the runtime Cuda 7 with the cuda 10 drivers. On the 8 >> core, runtime cuda 9.1 and cuda 10 drivers work well together - all with >> Gromacs 18.3. Now with Gromacs v19 , Cuda 10 and the 410 nvidia drivers, >> the 8 core and 32 core systems seem quite content. >> I have been tracing results from the log, and you are correct in what it can >> tell you. It was the log file that actually brought my attention to the >> Cuda 7 runtime issue. Also the PP PME distributions were noted with the >> ntomp/ntmpi arrangements. I have been experimenting with those as suggested >> in the Gromas acceleration hints. >> By 10% I meant that the 32 core unit ( in my hands ) ran 10% faster in >> ns/day than the 8 core AMD using the same model system and the the same >> 1080ti GPU. Gromacs points out that 150k to 300k atom systems are on the >> rather small side and so not to expect tremendous differences from the CPU. >> The reason for using the 32 core is the eventual addition of a second GPU >> and the subsequent distribution of threads. >> With a little OC and tweeking of the fourier spacing and vdw cutoffs in the >> npt I edged the 137k atom AHD model to 57 ns/day, but this falls short of >> the Exxact corp benchmarks of 80-90 ns/d — assuming they are using a >> 1080ti. Schrodinger’s Maestro- with the 8 core AMD and 1080ti - runs a >> 300k membrane model at about 15 ns/d but a 60k atom model at 150 ns/day >> implying 30 ns/day for 300k atoms. . In general, if I can indeed maintain >> 20-25 ns/day for 300k atoms I’d be satisfied. The original posts were made >> because I was frustrated seeing 6 to 8 ns/d with the 32core machine and the >> 8 core was producing 20 ns/day. As I mentioned the wounds were self >> inflicted with the installation of Cuda runtime 7 and at one point >> compilation with g++-5. As far as I am concerned it’s imperative that the >> latest drivers and Gromacs versions be used or at least the same genre of >> drivers and versions be assembled. >> Again, I’d like to point out that in using four different machines, 4 >> different Intel and AMD CPU’s, 5 different MBs, 5 different GPU’s, now 4 >> progressive versions of Gromacs, and model systems of 200-300 k particles, >> I’ve not run across a single problem associated with the software or >> hardware per se but rather was caused by the my models or my compilation >> methods. >> Hope this addresses your questions and helps any other users contemplating >> using a Ryzen TR. >> Paul >>> On Jan 3, 2019, at 2:09 PM, Tamas Hegedus wrote: >>> >>> Please provide more information. >>> >>> If you use gmx 2018 then I think that gmx limits the gcc version to 6 and >>> not cuda 10. >>> >>> You did not specify what type of and how many GPUs you use. >>> >>> In addition, the choice of gmx for distributing computation could be also >>> informative - you find this info in the log file. >>> >>> It is also not clear what do you mean of 10% improvement: 8ns/day to >>> 26ns/day are the only numbers but it corresponds to 3x faster simulations >>> and not 1.1x >>> >>> In addition, I think if you have 49.5 ns/day for 137K atoms than 26ns/day >>> seems to be ok for 300K. >>> >>> Bests, Tama
[gmx-users] free energy calculation for histone
Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate your good suggestions. Regards Ayesha Kanwal -- 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] Dihedral restraints
Thanks Mark for your reply In the log and edr files I only see an "Position Rest." term. So do you mean that the contributions on the dihedral restrains is added in in total energy without additional terms in the energy output in log file and the edr ? Thank you in advance for the clarification. Stéphane -- Message: 3 Date: Wed, 9 Jan 2019 12:32:31 +0100 From: Mark Abraham To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] Dihedral restraints Message-ID: Content-Type: text/plain; charset="UTF-8" Hi, IIRC that's enough, for dihedral restraints. You will see energy contributions from the the restraints appear in your .log and .edr files if the restraints are active. I don't recall if there is anything printed by mdrun before the simulation commences. Mark On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane wrote: > Hello > > I would like to apply some dihedral restraints in different residues of my > protein during the production stage. For that I have added at the end of > the protein itp the section > [ dihedral_restraints ]. Is it enough ? Should I add something else in the > mdp ? In other words, how to be sure that the restraints are effectively > applied during the run ? > > I am using GROMACS 2018.2 > > Thank in advance and happy new year to all > > St?phane > -- -- 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] Status of GROMACS native Windows Builds
Hi,
On Wed, Jan 9, 2019 at 4:54 PM Wahab Mirco <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> There was currently a thread regarding ways of using Gromacs on
> Windows systems. This cause me to try to download v.2019 to
> a Windows build machine and see what the NATIVE BUILD looks like.
>
> Installed on the Machine and used for the build were:
> - Visual Studio 2017 ("Visual Studio 15 Win64" in cmake)
> - fftw3f v.3.3.8, compiled in VS 2017 to a static library
> - boost 1.69.0
> (https://sourceforge.net/projects/boost/files/boost-binaries/)
>
BTW GROMACS hasn't used boost for quite a few years.
First, standard Gromacs without GPU acceleration and
> without external MPI (thread-MPI only). Using a CMD file:
>
>SET BOOST_ROOT=D:\usr\x64\boost_1_67_0
>SET BOOST_LIBRARYDIR=D:\usr\x64\boost_1_67_0\lib
>SET BOOST_INCLUDEDIR=D:\usr\x64\boost_1_67_0
>
>cmake -G "Visual Studio 15 Win64" ^
> -DCMAKE_INSTALL_PREFIX="D:/Gromacs2019" ^
> -DCMAKE_PREFIX_PATH="D:/Usr/x64"^
> -DGMX_GPU=OFF ^
> -DGMX_MPI=OFF ^
> -DFFTWF_LIBRARY=D:/Usr/x64/lib/libfftwf-3.3.8-vc141.lib ^
> -DCMAKE_BUILD_TYPE=Release ^
> ..\gromacs-2019
>
> and finally:
>
>devenv Gromacs.sln /build Release ^
>/project ALL_BUILD /projectconfig Release ^
>/project INSTALL
>
> created a 15 MB executable (gmx.exe) running flawlessly on the machine
> and appears reliable and fast.
>
Great! We test that kind of build in CI, so it should work, but we do not
ever look at the performance.
The build machine also has an old GTX-680 4GB with working CUDA 10 and
> working OpenCL 1.2. Neither a Cuda-Build nor an OpenCL build would
> succeed (see Appendix).
>
> Q: is further support for the windows platform to be expected?
>
Our major interests are the extra portability ensured by supporting MSVC
and its different C++ standard library. And later probably the Microsoft
correctness checking machinery, e.g. for the GSL.
We'd be likely to accept patches that would get the GPU support working,
but we won't prioritize effort to do it ourselves. Some of the type
mismatches look worth fixing on general principles, and e.g. if clFFT
doesn't support Windows, then we should fix our build stuff. I opened an
issue in our tracker.
Thanks!
Mark
Thanks & Regards
>
> M.
>
>
> ---
>
> Appendix:
>
> CUDA: cmake (3.13.2) would fail creating a makefile by complaining:
>
> -- Check for working NVCC/C compiler combination
> CMake Error at cmake/gmxManageNvccConfig.cmake:180 (message):
>message called with incorrect number of arguments
> Call Stack (most recent call first):
>cmake/gmxManageGPU.cmake:204 (include)
>CMakeLists.txt:590 (gmx_gpu_setup)
>
>
> -- Check for working NVCC/C compiler combination - broken
> CMake Error at cmake/gmxManageNvccConfig.cmake:185 (message):
>CUDA compiler does not seem to be functional.
> Call Stack (most recent call first):
>cmake/gmxManageGPU.cmake:204 (include)
>CMakeLists.txt:590 (gmx_gpu_setup)
>
>
>
> OpenCL: cmake detects OpenCL 1.2 and creates a makefile, but compilation
> fails at several places:
>
> 1>fft_binary_lookup.cpp
> 1>D:\LibSrc\Gromacs2019\gromacs-2019\src\external\clFFT\src\library\fft_binary_lookup.cpp(123):
>
> error C2664: 'HANDLE
> CreateFileA(LPCSTR,DWORD,DWORD,LPSECURITY_ATTRIBUTES,DWORD,DWORD,HANDLE)':
> cannot convert argument 1 from 'const _Elem *' to 'LPCSTR'
> 1>with
> 1>[
> 1>_Elem=wchar_t
> 1>]
> 1>D:\LibSrc\Gromacs2019\gromacs-2019\src\external\clFFT\src\library\fft_binary_lookup.cpp(129):
>
> note: Types pointed to are unrelated; conversion requires
> reinterpret_cast, C-style cast or function-style cast
> 1>Done building project "clFFT.vcxproj" -- FAILED.
> 2
>
> and
>
> 2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
>
> error C2672: 'std::max': no matching overloaded function found
> 2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
>
> error C2780: '_Ty std::max(std::initializer_list<_Elem>)': expects 1
> arguments - 2 provided
> 2>C:\Program Files (x86)\Microsoft Visual
> Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include\algorithm(5399):
> note: see declaration of 'std::max'
> 2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
>
> error C2782: 'const _Ty &std::max(const _Ty &,const _Ty &)
> noexcept()': template parameter '_Ty' is ambiguous
> 2>C:\Program Files (x86)\Microsoft Visual
> Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include\algorithm(5385):
> note: see declaration of 'std::max'
> 2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
>
> note: could be 'unsigned long'
> 2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(113
[gmx-users] Status of GROMACS native Windows Builds
There was currently a thread regarding ways of using Gromacs on
Windows systems. This cause me to try to download v.2019 to
a Windows build machine and see what the NATIVE BUILD looks like.
Installed on the Machine and used for the build were:
- Visual Studio 2017 ("Visual Studio 15 Win64" in cmake)
- fftw3f v.3.3.8, compiled in VS 2017 to a static library
- boost 1.69.0
(https://sourceforge.net/projects/boost/files/boost-binaries/)
First, standard Gromacs without GPU acceleration and
without external MPI (thread-MPI only). Using a CMD file:
SET BOOST_ROOT=D:\usr\x64\boost_1_67_0
SET BOOST_LIBRARYDIR=D:\usr\x64\boost_1_67_0\lib
SET BOOST_INCLUDEDIR=D:\usr\x64\boost_1_67_0
cmake -G "Visual Studio 15 Win64" ^
-DCMAKE_INSTALL_PREFIX="D:/Gromacs2019" ^
-DCMAKE_PREFIX_PATH="D:/Usr/x64"^
-DGMX_GPU=OFF ^
-DGMX_MPI=OFF ^
-DFFTWF_LIBRARY=D:/Usr/x64/lib/libfftwf-3.3.8-vc141.lib ^
-DCMAKE_BUILD_TYPE=Release ^
..\gromacs-2019
and finally:
devenv Gromacs.sln /build Release ^
/project ALL_BUILD /projectconfig Release ^
/project INSTALL
created a 15 MB executable (gmx.exe) running flawlessly on the machine
and appears reliable and fast.
The build machine also has an old GTX-680 4GB with working CUDA 10 and
working OpenCL 1.2. Neither a Cuda-Build nor an OpenCL build would
succeed (see Appendix).
Q: is further support for the windows platform to be expected?
Thanks & Regards
M.
---
Appendix:
CUDA: cmake (3.13.2) would fail creating a makefile by complaining:
-- Check for working NVCC/C compiler combination
CMake Error at cmake/gmxManageNvccConfig.cmake:180 (message):
message called with incorrect number of arguments
Call Stack (most recent call first):
cmake/gmxManageGPU.cmake:204 (include)
CMakeLists.txt:590 (gmx_gpu_setup)
-- Check for working NVCC/C compiler combination - broken
CMake Error at cmake/gmxManageNvccConfig.cmake:185 (message):
CUDA compiler does not seem to be functional.
Call Stack (most recent call first):
cmake/gmxManageGPU.cmake:204 (include)
CMakeLists.txt:590 (gmx_gpu_setup)
OpenCL: cmake detects OpenCL 1.2 and creates a makefile, but compilation
fails at several places:
1>fft_binary_lookup.cpp
1>D:\LibSrc\Gromacs2019\gromacs-2019\src\external\clFFT\src\library\fft_binary_lookup.cpp(123):
error C2664: 'HANDLE
CreateFileA(LPCSTR,DWORD,DWORD,LPSECURITY_ATTRIBUTES,DWORD,DWORD,HANDLE)':
cannot convert argument 1 from 'const _Elem *' to 'LPCSTR'
1>with
1>[
1>_Elem=wchar_t
1>]
1>D:\LibSrc\Gromacs2019\gromacs-2019\src\external\clFFT\src\library\fft_binary_lookup.cpp(129):
note: Types pointed to are unrelated; conversion requires
reinterpret_cast, C-style cast or function-style cast
1>Done building project "clFFT.vcxproj" -- FAILED.
2
and
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
error C2672: 'std::max': no matching overloaded function found
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
error C2780: '_Ty std::max(std::initializer_list<_Elem>)': expects 1
arguments - 2 provided
2>C:\Program Files (x86)\Microsoft Visual
Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include\algorithm(5399):
note: see declaration of 'std::max'
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
error C2782: 'const _Ty &std::max(const _Ty &,const _Ty &)
noexcept()': template parameter '_Ty' is ambiguous
2>C:\Program Files (x86)\Microsoft Visual
Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include\algorithm(5385):
note: see declaration of 'std::max'
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
note: could be 'unsigned long'
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
note: or 'size_t'
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
error C2784: 'const _Ty &std::max(const _Ty &,const _Ty &)
noexcept()': could not deduce template argument for 'const _Ty &'
from 'unsigned long'
2>C:\Program Files (x86)\Microsoft Visual
Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include\algorithm(5385):
note: see declaration of 'std::max'
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
error C2784: '_Ty std::max(std::initializer_list<_Elem>,_Pr)': could not
deduce template argument for 'std::initializer_list<_Elem>' from 'size_t'
2>C:\Program Files (x86)\Microsoft Visual
Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include\algorithm(5375):
note: see declaration of 'std::max'
2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135):
error C2780: 'const _Ty &std::max(const _Ty &,const _Ty &,_
[gmx-users] gromacs 2016.3 solvate error for methanol water mixture
Dear gromacs-users, I generated and equilibrated a box (4 x 4 x 4 nm) containing a mixture of water and methanol. With this I wanted to solvate my protein: gmx solvate -cp protein.gro -cs wat-methanol.gro -o prot_solv.gro -p topol.top However, this results in an error starting with: *** Error in `gmx_mpi': free(): invalid pointer: 0x0364d1c0 *** Has anyone experienced this before? Has anyone a suggestion what might have gone wrong? Thank you very much in advance. All the best Johannes __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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] Driver 410 solved the issue. Re: Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI
Dear Paul and Mark, Thank you for the suggestions. I just upgraded NVIDIA driver from 384 to 410 and the problem is solved. Regards, Adarsh V. K. -- Message: 6 Date: Tue, 8 Jan 2019 18:29:18 -0600 From: paul buscemi To: "gmx-us...@gromacs.org" Subject: Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI Message-ID: <639c609a-1675-4848-bbad-2748e96a7...@q.com> Content-Type: text/plain; charset=utf-8 I just built from a similar situation but also went to Ubuntu Mint Tara 19 , cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not install the driver from the toolkit ) added the 410 driver from the PPA and the system is quite happy. I believe I ran across some information that suggests that the mixture of Runtime 8, Cuda driver 9 and Ubuntu 16 is not a good mix. I?ll try to look for it later if you need further information Paul --- From: Adarsh V. K. Date: Wed, Jan 9, 2019 at 1:03 AM Subject: Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI To: Dear all, recently upgraded Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04 with a new GPU GTX1080TI. CUDA from 7.5 to 8. Driver 384. Problem: GPU not detected during MD run. Details are as follows: 1) Running on 1 node with total 8 cores, 8 logical cores, 0 compatible GPUs Hardware detected: But deviceQuery as follows 2) ./deviceQuery ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) Detected 1 CUDA Capable device(s) Device 0: "GeForce GTX 1080 Ti" CUDA Driver Version / Runtime Version 9.0 / 8.0 CUDA Capability Major/Minor version number:6.1 Total amount of global memory: 11169 MBytes (11711807488 bytes) (28) Multiprocessors, (128) CUDA Cores/MP: 3584 CUDA Cores GPU Max Clock rate:1658 MHz (1.66 GHz) Memory Clock rate: 5505 Mhz Memory Bus Width: 352-bit L2 Cache Size: 2883584 bytes Maximum Texture Dimension Size (x,y,z) 1D=(131072), 2D=(131072, 65536), 3D=(16384, 16384, 16384) Maximum Layered 1D Texture Size, (num) layers 1D=(32768), 2048 layers Maximum Layered 2D Texture Size, (num) layers 2D=(32768, 32768), 2048 layers Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per multiprocessor: 2048 Maximum number of threads per block: 1024 Max dimension size of a thread block (x,y,z): (1024, 1024, 64) Max dimension size of a grid size(x,y,z): (2147483647, 65535, 65535) Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Concurrent copy and kernel execution: Yes with 2 copy engine(s) Run time limit on kernels: Yes Integrated GPU sharing Host Memory:No Support host page-locked memory mapping: Yes Alignment requirement for Surfaces:Yes Device has ECC support:Disabled Device supports Unified Addressing (UVA): Yes Device PCI Domain ID / Bus ID / location ID: 0 / 1 / 0 Compute Mode: < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 9.0, CUDA Runtime Version = 8.0, NumDevs = 1, Device0 = GeForce GTX 1080 Ti Result = PASS -- 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] calculate interaction energy between two proteins
On 1/9/19 3:31 AM, SHAHEE ISLAM wrote: it is connected with aggregation phenomenon. Maybe, but no force field is parametrized with protein aggregation in mind. Mark is cautioning you that you may be seeking a meaningless quantity. To calculate the interaction energy, you need to define energygrps in your .mdp file (each protein in a separate group), generate a new .tpr file, then use mdrun -rerun to re-evaluate the energies with these groups from the existing trajectory. Then it is your job to convince your skeptical audience that such a quantity actually means anything. -Justin On 1/9/19, Mark Abraham wrote: Hi, How is the protein-protein interaction energy defined? What physical observable is it connected to? Mark On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM wrote: can anyone please tell me, if i select 42 then wheather it will calculate the protein-protein interaction energy? because i did not define two proteins in the mdp file.i just mentioned protein.I am not understanding this. thanking you On 1/8/19, SHAHEE ISLAM wrote: hi, i want to calculate interaction energy between two protein. In my system there are two proteins,waters and ions.In my .mdp file the, energygrps = PROTEIN W ION i am using this command gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg then the following options are coming 1 Bond 2 G96Angle 3 Proper-Dih. 4 Improper-Dih. 5 LJ-(SR) 6 Coulomb-(SR) 7 Potential8 Kinetic-En. 9 Total-Energy10 Temperature 11 Pressure12 Constr.-rmsd 13 Box-X 14 Box-Y 15 Box-Z 16 Volume 17 Density 18 pV 19 Enthalpy20 Vir-XX 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 Vir-YY 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 Vir-ZZ 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 Pres-YX 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 Pres-ZY 37 Pres-ZZ 38 #Surf*SurfTen 39 Box-Vel-XX 40 Box-Vel-YY 41 Box-Vel-ZZ 42 Coul-SR:Protein-Protein 43 LJ-SR:Protein-Protein 44 Coul-SR:Protein-W 45 LJ-SR:Protein-W 46 Coul-SR:Protein-ION 47 LJ-SR:Protein-ION 48 Coul-SR:W-W 49 LJ-SR:W-W 50 Coul-SR:W-ION 51 LJ-SR:W-ION 52 Coul-SR:ION-ION 53 LJ-SR:ION-ION 54 T-Protein 55 T-W 56 T-ION 57 Lamb-Protein58 Lamb-W 59 Lamb-ION if i select 42 and 43. will it give me the total energy value considering both proteins. or what should i correctly select. thanking you Shahee Islam -- 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. -- == 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] RMSD plots protein-peptide complex
On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. Make an index group that includes only the atoms you want to analyze. -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] ramachandran plot
Hi Javed, I hope *gmx rama* will solve the issue. http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* DBT Research Associate, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subho...@yahoo.com On Wed, Jan 9, 2019 at 3:01 PM wrote: > Dear Users > > Can anyone suggest me any available tool to analyze ramachandran plot > timewise for a trajectory? > > Thank You > > Regards > Zaved Hazarika > Research Scholar > Dept. Of Molecular Biology and Biotechnology, > Tezpur University, > India > > > > > > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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] Dihedral restraints
Hi, IIRC that's enough, for dihedral restraints. You will see energy contributions from the the restraints appear in your .log and .edr files if the restraints are active. I don't recall if there is anything printed by mdrun before the simulation commences. Mark On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane wrote: > Hello > > I would like to apply some dihedral restraints in different residues of my > protein during the production stage. For that I have added at the end of > the protein itp the section > [ dihedral_restraints ]. Is it enough ? Should I add something else in the > mdp ? In other words, how to be sure that the restraints are effectively > applied during the run ? > > I am using GROMACS 2018.2 > > Thank in advance and happy new year to all > > Stéphane > -- > 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] RMSD plots protein-peptide complex
Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. Thanks in anticipation -- 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] ramachandran plot
Hi, I use the python MDAnalysis packages for this. https://github.com/MDAnalysis/mdanalysis/issues/1335 https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html Have a nice day, Tamas On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.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] Help with gmx select
Hello, I want to use gmx select to get a list of protein residues that interact with PO4 beads (CG) in a bilayer: The command I am using is: gmx select -s system.gro -f traj.xtc -oi contacting_residues_DOPG.dat -resnr number -n PO4_index_1.ndx -select 'group Protein and same residue as within 0.6 of (group PO4_DOPG_upper or group PO4_DOPG_lower)' But it returns the list of all atoms numbers of every interacting residue. I want ONLY the residue number. Any idea? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- 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] RDF in gromacs
Hi, I am calculating the rdf of my system as follows. 1. rdf of oxygen atom of my drug and water this is successful (I just made an index file and for water i choose eg. 5 & a OW) this worked fine. 2. I want now to calculate the rdf of oxygen in my drug and oxygen from the hydroxyl group of the chitosan, I am getting difficult on how to select only oxygen in chitosan or polymer and make an index file, I am getting syntax errors, How should I do? Help. -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- 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] ramachandran plot
Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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] Dihedral restraints
Hello I would like to apply some dihedral restraints in different residues of my protein during the production stage. For that I have added at the end of the protein itp the section [ dihedral_restraints ]. Is it enough ? Should I add something else in the mdp ? In other words, how to be sure that the restraints are effectively applied during the run ? I am using GROMACS 2018.2 Thank in advance and happy new year to all Stéphane -- 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] failing of g_membed
Thank you for your replay. I will check it out On Wed, Jan 9, 2019 at 6:58 AM Mark Abraham wrote: > Hi, > > As I'm sure you know from reading up on membed, it works by scaling the > embedded protein to be tiny and turning off its interactions. The mostly > likely issue is that you didn't give those instructions correctly. Double > check the documentation, and use a recent version of GROMACS to get the bug > fixes that have happened since your version, which I can see is several > years old. > > Mark > > On Tue, Jan 8, 2019 at 9:21 AM Netaly Khazanov wrote: > > > Hi All, > > I have an aligned structure of protein+ligands in the membrane (a mixture > > of DPPC and DOPC). > > The structure is solvated with water (gmx solvate -cp > > protein_ATP_membrane_box.gro -cs -o protein_ATP_membrane_box_solv.gro -p > > topol1.top) > > And I used it as input file for g_membed. > > grompp_d -c protein_ATP_membrane_box_solv.gro -p topol1.top -f membed.mdp > > -o membed.tpr -n > > g_membed_d -f membed.tpr -p topol1.top -o membed_out.trr -x > membed_out.xtc > > -c membed_out.gro -e -n -xyinit 0.1 -xyend 1.0 -nxy 1000 or > > g_membed_d -f membed.tpr -p topol1.top -o membed_out.trr -x > membed_out.xtc > > -c membed_out.gro -e -n -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend > > 1.0 -nz 100 > > it fails with Fatal error: > > Step 0, time 0 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 175118.647912, max 39729618.834230 (between atoms 86781 and 86783) > > bonds that rotated more than 90 degrees: > > > > Too many LINCS warnings (9639) > > If you know what you are doing you can adjust the lincs warning threshold > > in your mdp file > > I tried to reduce the time step, it didn't help. > > Where should it look in my structure. It is obvious that there are a lot > of > > overlapping atoms of protein with membrane/water. > > Thank you for any help. > > Netaly > > > > > > -- > > Netaly > > -- > > 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. > -- Netaly -- 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] calculate interaction energy between two proteins
it is connected with aggregation phenomenon. On 1/9/19, Mark Abraham wrote: > Hi, > > How is the protein-protein interaction energy defined? What physical > observable is it connected to? > > Mark > > On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM wrote: > >> can anyone please tell me, if i select 42 then wheather it will >> calculate the protein-protein interaction energy? because i did not >> define two proteins in the mdp file.i just mentioned protein.I am not >> understanding this. >> thanking you >> >> On 1/8/19, SHAHEE ISLAM wrote: >> > hi, >> > i want to calculate interaction energy between two protein. >> > In my system there are two proteins,waters and ions.In my .mdp file >> > the, energygrps = PROTEIN W ION >> > i am using this command >> > gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg >> > then the following options are coming >> > >> > 1 Bond 2 G96Angle 3 Proper-Dih. 4 >> > Improper-Dih. >> > 5 LJ-(SR) 6 Coulomb-(SR) 7 Potential8 >> > Kinetic-En. >> > 9 Total-Energy10 Temperature 11 Pressure12 >> > Constr.-rmsd >> > 13 Box-X 14 Box-Y 15 Box-Z 16 Volume >> > 17 Density 18 pV 19 Enthalpy20 Vir-XX >> > 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 Vir-YY >> > 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 Vir-ZZ >> > 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 >> > Pres-YX >> > 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 >> > Pres-ZY >> > 37 Pres-ZZ 38 #Surf*SurfTen 39 Box-Vel-XX 40 >> Box-Vel-YY >> > 41 Box-Vel-ZZ 42 Coul-SR:Protein-Protein >> > 43 LJ-SR:Protein-Protein 44 Coul-SR:Protein-W >> > 45 LJ-SR:Protein-W 46 Coul-SR:Protein-ION >> > 47 LJ-SR:Protein-ION 48 Coul-SR:W-W >> > 49 LJ-SR:W-W 50 Coul-SR:W-ION >> > 51 LJ-SR:W-ION 52 Coul-SR:ION-ION >> > 53 LJ-SR:ION-ION 54 T-Protein 55 T-W 56 T-ION >> > 57 Lamb-Protein58 Lamb-W 59 Lamb-ION >> > >> > if i select 42 and 43. will it give me the total energy value >> > considering both proteins. >> > or what should i correctly select. >> > thanking you >> > Shahee Islam >> > >> -- >> 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.
Re: [gmx-users] calculate interaction energy between two proteins
Hi, How is the protein-protein interaction energy defined? What physical observable is it connected to? Mark On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM wrote: > can anyone please tell me, if i select 42 then wheather it will > calculate the protein-protein interaction energy? because i did not > define two proteins in the mdp file.i just mentioned protein.I am not > understanding this. > thanking you > > On 1/8/19, SHAHEE ISLAM wrote: > > hi, > > i want to calculate interaction energy between two protein. > > In my system there are two proteins,waters and ions.In my .mdp file > > the, energygrps = PROTEIN W ION > > i am using this command > > gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg > > then the following options are coming > > > > 1 Bond 2 G96Angle 3 Proper-Dih. 4 > > Improper-Dih. > > 5 LJ-(SR) 6 Coulomb-(SR) 7 Potential8 > > Kinetic-En. > > 9 Total-Energy10 Temperature 11 Pressure12 > > Constr.-rmsd > > 13 Box-X 14 Box-Y 15 Box-Z 16 Volume > > 17 Density 18 pV 19 Enthalpy20 Vir-XX > > 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 Vir-YY > > 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 Vir-ZZ > > 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 Pres-YX > > 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 Pres-ZY > > 37 Pres-ZZ 38 #Surf*SurfTen 39 Box-Vel-XX 40 > Box-Vel-YY > > 41 Box-Vel-ZZ 42 Coul-SR:Protein-Protein > > 43 LJ-SR:Protein-Protein 44 Coul-SR:Protein-W > > 45 LJ-SR:Protein-W 46 Coul-SR:Protein-ION > > 47 LJ-SR:Protein-ION 48 Coul-SR:W-W > > 49 LJ-SR:W-W 50 Coul-SR:W-ION > > 51 LJ-SR:W-ION 52 Coul-SR:ION-ION > > 53 LJ-SR:ION-ION 54 T-Protein 55 T-W 56 T-ION > > 57 Lamb-Protein58 Lamb-W 59 Lamb-ION > > > > if i select 42 and 43. will it give me the total energy value > > considering both proteins. > > or what should i correctly select. > > thanking you > > Shahee Islam > > > -- > 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] calculate interaction energy between two proteins
can anyone please tell me, if i select 42 then wheather it will calculate the protein-protein interaction energy? because i did not define two proteins in the mdp file.i just mentioned protein.I am not understanding this. thanking you On 1/8/19, SHAHEE ISLAM wrote: > hi, > i want to calculate interaction energy between two protein. > In my system there are two proteins,waters and ions.In my .mdp file > the, energygrps = PROTEIN W ION > i am using this command > gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg > then the following options are coming > > 1 Bond 2 G96Angle 3 Proper-Dih. 4 > Improper-Dih. > 5 LJ-(SR) 6 Coulomb-(SR) 7 Potential8 > Kinetic-En. > 9 Total-Energy10 Temperature 11 Pressure12 > Constr.-rmsd > 13 Box-X 14 Box-Y 15 Box-Z 16 Volume > 17 Density 18 pV 19 Enthalpy20 Vir-XX > 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 Vir-YY > 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 Vir-ZZ > 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 Pres-YX > 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 Pres-ZY > 37 Pres-ZZ 38 #Surf*SurfTen 39 Box-Vel-XX 40 Box-Vel-YY > 41 Box-Vel-ZZ 42 Coul-SR:Protein-Protein > 43 LJ-SR:Protein-Protein 44 Coul-SR:Protein-W > 45 LJ-SR:Protein-W 46 Coul-SR:Protein-ION > 47 LJ-SR:Protein-ION 48 Coul-SR:W-W > 49 LJ-SR:W-W 50 Coul-SR:W-ION > 51 LJ-SR:W-ION 52 Coul-SR:ION-ION > 53 LJ-SR:ION-ION 54 T-Protein 55 T-W 56 T-ION > 57 Lamb-Protein58 Lamb-W 59 Lamb-ION > > if i select 42 and 43. will it give me the total energy value > considering both proteins. > or what should i correctly select. > thanking you > Shahee Islam > -- 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.
