Hi all,
I recently started using HMR with 4fs timestep at the suggestion of the
amber community.
I used parmed's hmassrepartition command to repartition.
My systems are equilibrated with the amberMDprep protocol, which uses a 1
fs time step with SHAKE.
If I use a 4 fs time step for production, my simulations crash within a few
nanoseconds, if I restart these simulations they will run for a few
nanoseconds before crashing again.
If I use a 2 fs time step with HMR I don't have this issue.
I am using ff19SB with OPC on amber 18. I am not repartitioning water. I've
also included an example input for production below. My system is about
600,000 atoms
Is there something else I should be doing to make my HMR simulations more
stable?
-Neville
&cntrl
imin = 0, nstlim = 500000, dt = 0.004,
ntx = 5, irest = 1, ig = -1,
ntwx = 50000, ntwv = -1, ioutfm = 1, ntxo = 2, ntpr = 50000, ntwr =
50000,
iwrap = 1, nscm = 1000, vlimit = 10.0,
ntc = 2, ntf = 2, ntb = 2, cut = 10.0,
ntt = 3, gamma_ln = 5, temp0 = 298.0, tempi = 298.0,
ntp = 1, barostat = 2, pres0 = 1.0, mcbarint = 100,
ntr = 0,
&end
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Received on Mon Jun 07 2021 - 10:00:03 PDT
