[gmx-users] nitrogen itp file with virtual site
Hello GROMACS users, This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at super critical point.The structure I use is different from regular nitrogen (N-N). As you know N atom has a negative charge which means the nitrogen molecule will be negatively charged, therefore I need to use massless and charged virtual site to equilibrate the molecule. I have looked on the tutorial about CO2 to produce the XXX.itp but didnot work with me. Could anyone have done it before tell me how to do it ? Here are the parameters: N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge =(-0.482 e). XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge= 0.964 e. Thank you very much. -- 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] Regarding precision in gromacs
Hello, i have installed gromacs 2016.2, and in the command line if i type gmx --version i am getting as:- GROMACS version:2016.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:disabled SIMD instructions: AVX2_256 FFT library:fftw-3.3.3-sse2-avx RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled Built on: Sun Jul 16 13:28:27 IST 2017 Built by: root@DILIP [CMAKE] Build OS/arch: Linux 3.13.0-24-generic x86_64 Build CPU vendor: Intel Build CPU brand:Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz Build CPU family: 6 Model: 60 Stepping: 3 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU 4.8.4 C compiler flags:-march=core-avx2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 4.8.4 C++ compiler flags: -march=core-avx2-std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast My doubt is tht how does the precision have any effect on the simulation..?? and how can i convert/make the gromacs version tht i have installed(2016.2), from single precision to double precision...?? what are the commands tht i need to give ...?? Thank you... -- With Best Regards, DILIP.H.N Ph.D Student -- 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.
