Dear All,
I am trying to simulate thermodynamic integration tutorials with pmemd.cuda
(GPU) implemented in Amber18.
In tutorials (A9),
there are three steps (discharge, vdw-bonded, recharge).
In vdw-bonded step, I got error messages.
In discharge or recharge steps, I didn't get error messages.
When I compared to input files in discharge and recharge steps,
there are only differences in next sentence.
<discharge> or <recharge>
ifsc=0, crgmask=':1.O1,H6',
<vdw_bonded>
ifsc=1, scmask1=':1.H6', scmask2=':2.O1,H6', crgmask=':1.H6 | :2.O1,H6'
What value should I set for mbar_states and mbar_lambda ?
The error messages follow.
Note: ig = -1. Setting random seed to 75620 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
| ERROR: mbar_states not set, please set mbar_states to the number of
lambdas you wish sample
| ERROR: mbar_lambda not set, please set mbar_lambda to the lambdas you
wish to sample
| ERROR: bar_l_min/max/incr are deprecated. please put all lambdas you
wish to sample in mbar_lambda and set mbar_states = the total number of
lambdas
Input errors occurred. Terminating execution.
input file (ti.in) follows.
TI simulation
&cntrl
imin = 0, nstlim = 100000, irest = 1, ntx = 5, dt = 0.002,
ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
ntc = 2, ntf = 1,
ntb = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 10000, ntpr = 10000, ntwr = 20000,
icfe = 1, clambda = 1.0, scalpha = 0.5, scbeta = 12.0,
logdvdl = 1,
ifmbar = 1, bar_intervall = 1000, bar_l_min = 0.0, bar_l_max = 1.0,
bar_l_incr = 0.1,
timask1 = ':1', timask2 = ':2',
ifsc=1, scmask1=':1.H6', scmask2=':2.O1,H6', crgmask=':1.H6 | :2.O1,H6'
/
&ewald
/
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Received on Mon Sep 23 2019 - 19:00:01 PDT
