Hi all,
I'm having an unusual situation where I have a single nucleoside (DTN in this case) in a water box with salt on Amber16, but it keeps crashing during production. I went back and double checked, and noticed there was some very odd behavior with void bubbles forming during the initial minimization (attached), ie if I run it with
mpirun --bind-to core -np 6 ${AMBERHOME}/amber16/bin/pmemd.MPI -O -i 01a_sol_min.in -p *.prmtop -c *.inpcrd -o 01a_sol_min.out -r 01a_sol_min.rst -ref *.inpcrd
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 1000,
ntmin = 1,
ntb = 1,
ntr = 1,
ntpr = 500,
cut = 8.0
/
Hold only DNA+protein fixed
500.0
RES 1 1
END
END
Some very large gaps form in the solvent which by the point it hits production I'm guessing it can't resolve, but I can't think of why that'd be? I did a fairly standard setup for the system with
source leaprc.DNA.OL15
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
m1 = loadpdb DTN_21.pdb
solvateOct m1 TIP3PBOX 10.0 iso 1.0
addIons m1 Na+ 0
addIons m1 Cl- 0
addIonsRand m1 Na+ 2
addIonsRand m1 Cl- 2
saveamberparm m1 DTN_21.prmtop DTN_21.inpcrd
savepdb m1 check_DTN_21.pdb
quit
I've managed to get other nucleosides to finish without any issues so far, but I'm scratching my head of what'd be wrong, or if I had missed something obvious?
Best,
Kenneth
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Received on Wed Feb 02 2022 - 10:30:02 PST
