GROMACS version: 2023.3
GROMACS modification: No
About my soft : I installed Gromacs 2023.3 on windows with Cuda using an NVIDIA RTA3000A which is detected by Gromacs.
I’m following the tutorial on mdtutorials.com, ond when the time come to start the run, nothing, the command start but it show :
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
And done, no calculation…
Any help on this :
I’ve dropped all the file used here in this Google drive file, If you need any information or document, do not hesitate.
Thanks in advance for your help.
Jules F.
No, I get exactly the same thing that is on the picture up there.
As well as the files generated, em.edr, em.trr are generated but empty, as well as em.log which end up with this:
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using GPU 8x8 nonbonded short-range kernels
Using a 8x8 pair-list setup:
updated every 1 steps, buffer 0.000 nm, rlist 1.200 nm
Removing pbc first time
Pinning threads with an auto-selected logical cpu stride of 1
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- — Thank You — -------- --------
No, I get exactly the same result than the one on the picture up there.
3 files are also generated : em.trr and em.edr, both empty and an em.log which end with this :
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using GPU 8x8 nonbonded short-range kernels
Using a 8x8 pair-list setup:
updated every 1 steps, buffer 0.000 nm, rlist 1.200 nm
Removing pbc first time
Pinning threads with an auto-selected logical cpu stride of 1
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- — Thank You — -------- --------
I encountered the same issue. I compiled the Windows versions (2023.4 and 2024) myself, and there were no problems during the compilation process. However, every time I reached this step, I encountered the same results as you
I also checked my compilation process. Although I ultimately obtained gmx.exe, there were ‘errors’ in the progress. I believe the issues I encountered while running mdrun might be related to these errors
I wonder if you encountered similar errors, even though ended up with a runnable program
example1
– Looking for include file pwd.h - not found
– Looking for include file dirent.h
– Looking for include file dirent.h - not found
– Looking for include file time.h
– Looking for include file time.h - found
– Looking for include file sys/time.h
– Looking for include file sys/time.h - not found
– Looking for include file io.h
– Looking for include file io.h - found
– Looking for include file sched.h
– Looking for include file sched.h - not found
– Looking for include file xmmintrin.h
– Looking for include file xmmintrin.h - found
– Looking for gettimeofday
– Looking for gettimeofday - not found
– Looking for sysconf
– Looking for sysconf - not found
– Looking for nice
– Looking for nice - not found
– Looking for fsync
– Looking for fsync - not found
– Looking for _fileno
– Looking for _fileno - found
– Looking for fileno
– Looking for fileno - found
– Looking for _commit
– Looking for _commit - found
– Looking for sigaction
– Looking for sigaction - not found
– Performing Test HAVE_BUILTIN_CLZ
– Performing Test HAVE_BUILTIN_CLZ - Failed
– Performing Test HAVE_BUILTIN_CLZLL
– Performing Test HAVE_BUILTIN_CLZLL - Failed
example2
– Could NOT find LAPACK (missing: LAPACK_LIBRARIES)
Reason given by package: LAPACK could not be found because dependency BLAS could not be found.
