Dear Amber users,
I'm facing an interesting issue with Amber22.
I want to use the 12-6-4 LJ parameters for my system, using the following
tutorial: https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php
I prepared the system using the frcmod.ions234lm_1264_tip3p for my system
solvated in TIP3P water model. I generated the .inpcrd and .prmtop files
without any errors using tLeaP.
Then I used parmed to add the C coefficient parameters to the system.
Parmed did not report any issues with the files.
But when I tried to run minimization on the system, I'm seeing a
segmentation fault error and the output of the minimization ends at the
following line:
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 1, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 2500, ntrx = 1, ntwr =
1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
lj1264 = 1
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 50.00000
Energy minimization:
maxcyc = 100000, ncyc = 10, ntmin = 2
dx0 = 0.01000, drms = 0.00010
However, when I use the first generated .prmtop file, without the C
coefficient, the minimization on GPU runs smoothly. Also, when I switch
from pmemd.cuda to pmemd.MPI it seems to run OK, but then it's super slow.
I'm running out of ideas of what else I can check or change in my setup.
Maybe someone here had the same issue and could give me a hand?
Looking forward to any help.
Best regards,
Karolina Mitusińska
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Received on Sat Aug 02 2025 - 11:00:03 PDT
