From: shreya bhattacharya (shreya199713_at_gmail.com)
Date: Sat Sep 10 2022 - 02:31:01 CDT
Hi,
I am currently trying to run FEP simulation in NAMD 3.0 alpha 10 GPU. I
have no problem doing equilibration. But at the very beginning of the
simulation I get an error as shown below
ERROR: Atoms moving too fast at timestep 964; simulation has become
unstable (0 atoms on pe 0).
FATAL ERROR: SequencerCUDA: Atoms moving too fast
Even in the fepout file, the temperature suddenly increases abnormally.
# STEP Elec vdW
dE dE_avg Temp dG
# l l+dl l
l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.02
FepEnergy: 50 -165910.5381 -165902.7090 12441.2784
12439.7735 6.3242 5.9923 309.0416 5.9923
FepEnergy: 100 -165702.8932 -165695.0942 12447.1530
12445.2748 5.9208 5.9923 310.6974 5.9923
FepEnergy: 150 -165016.7630 -165009.4752 12045.5977
12044.0162 5.7063 5.9923 311.4188 5.9923
FepEnergy: 200 -165692.9779 -165685.3490 12609.5741
12607.6336 5.6884 5.9923 311.9251 5.9923
FepEnergy: 250 -165035.2737 -165027.7933 11862.7841
11861.0165 5.7128 5.9923 312.2674 5.9923
FepEnergy: 300 -165258.8857 -165251.1882 12082.2996
12080.6978 6.0957 5.9923 310.8036 5.9923
FepEnergy: 350 -165041.5087 -165033.7478 11987.9307
11986.5414 6.3716 5.9923 311.3459 5.9923
FepEnergy: 400 -165967.1586 -165959.4883 12603.3140
12601.4027 5.7590 5.9923 312.5948 5.9923
FepEnergy: 450 -164708.4792 -164700.3822 11676.2268
11674.3472 6.2173 5.9923 310.0378 5.9923
FepEnergy: 500 -166719.3720 -166711.1859 13116.8221
13115.0177 6.3817 5.9923 314.2613 5.9923
FepEnergy: 550 -164147.7088 -164139.5909 11186.4004
11184.2780 5.9954 5.9923 310.0295 5.9923
FepEnergy: 600 -167708.1021 -167700.4099 13926.5939
13924.9991 6.0974 5.9923 316.8016 5.9923
FepEnergy: 650 -162516.1529 -162508.9654 10059.9600
10058.7121 5.9396 5.9923 308.6390 5.9923
FepEnergy: 700 -169208.9565 -169201.3722 15459.2323
15457.8658 6.2178 5.9923 321.4258 5.9923
FepEnergy: 750 -158689.9256 -158682.1162 7743.3810
7742.3172 6.7456 5.9923 315.2326 5.9923
FepEnergy: 800 -172104.0666 -172095.8031 19128.7743
19125.8741 5.3632 5.9923 350.0649 5.9923
FepEnergy: 850 -149910.8960 -149903.4472 4169.0670
4167.9828 6.3646 5.9923 353.6883 5.9923
FepEnergy: 900 -175764.9272 -175757.0855 27105.3806
27103.0027 5.4639 5.9923 469.5948 5.9923
FepEnergy: 950 -111497.4204 -111491.9815 -3498.4888
-3498.5603 5.3675 5.9923 769.8944 5.9923
With no atom listed, NAMD doesn’t exit but instead hangs.
Can someone help me on how to solve this error?
Has anyone successfully done FEP simulation in NAMD3? Can you guide me on
what are the changes I need to make in the configurarion file other than
adding CUDASOAintegrate on?
Thank you in advance!
-- *Regards,* *Shreya Bhattacharya*
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