Hi Åsmund Røhr Kjendseth,
Can you make sure if the CUDA version of Amber is recompiled after all
updates are applied? In addition, after recompilation, you could run the
cuda test to make sure the compilation is okay and ff19SB is enabled in
pmemd.cuda.
You could go to the directory $AMBERHOME/test/cuda/ff19SB/, and execute
./Run SPFP and ./Run DPFP and check if both tests pass.
Let me know if this works!
Thank you!
Chuan
On Wed, Oct 16, 2019 at 9:10 AM Åsmund Røhr Kjendseth <asmund.rohr.nmbu.no>
wrote:
> Dear developers,
>
> I just recompiled AmberTools 19 and Amber 18 with the last upgrades to
> enable simulations with the ff19SB FF. In the initial minimization the
> information below (including the CMAP term) is printed. However, when
> running pmemd (CUDA version) no CMAP information whatsoever is printed.
> update_amber tells me that no additional updates are available.
>
> Maybe the CUDA version isn’t updated yet?
>
> Cheers,
>
> Åsmund Røhr Kjendseth
>
>
> | CMAP information read from topology file:
>
> | Memory Use Allocated
> | Real 7195896
> | Hollerith 278957
> | Integer 4120458
> | Max Pairs 4970995
> | nblistReal 1035624
> | nblist Int 2972152
> | Total 112521 kbytes
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
> |CMAP: Reticulating splines.
>
> ………
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 -3.4871E+05 1.1031E-01 1.1542E+01 CD 5466
>
> BOND = 68530.4819 ANGLE = 1311.1021 DIHED =
> 2237.4689
> VDWAALS = 81088.9513 EEL = -525260.1112 HBOND =
> 0.0000
> 1-4 VDW = 1627.8336 1-4 EEL = 21433.1020 RESTRAINT =
> 0.0000
> CMAP = 321.0570
>
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>
--
*Chuan Tian*
*Ph.D Candidate*
*Carlos Simmerling Laboratory*
*Department of Chemistry*
*Laufer Center for Physical and Quantitative Biology*
*Stony Brook University*
*chuan.tian.1.stonybrook.edu <thomas.allison.stonybrook.edu>*
*tianchuan1015.gmail.com <rockhemisphere.gmail.com>*
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Received on Wed Oct 16 2019 - 07:30:01 PDT
