[AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU)

From: HOCHEOL LIM <ihcdatabank.gmail.com>
Date: Tue, 24 Sep 2019 10:35:20 +0900

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
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