1. Try the [ bonds ] section that I mentioned earlier and remove the [
constraints ] section.
2. Did you do an energy minimization? If so, what total Energy and max
force do you acheive?
3. What is the size of your box? Is it >=3.0nm? Is that also larger
than 1.49 + max_n-hexadecane_length? It should be both of these,
although only the first issue is likely to show up as an energy error.
4. What vdwtype and coulombtype are you using? This might be problematic:
rcoulomb = 1.49
rlist = 1.38
rvdw = 1.38
Try this instead:
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
vdwtype = cut-off
rvdw_switch = 0
rvdw = 1.4
rlist = 0.9
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