[gmx-users] Regarding precision in gromacs

Justin Lemkul jalemkul at vt.edu
Mon Jul 17 15:39:59 CEST 2017

On 7/16/17 1:39 PM, Dilip H N wrote:
> 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 at 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 ...??

You need to reinstall in double precision.  There are only a few specific cases 
that actually require full, double precision (GROMACS uses mixed by default and 
all the critical calculations are already in double).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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