[AMBER] significance of iwrap

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Fri, 1 Sep 2017 11:59:28 +0000 (UTC)

Dear all,
Currently I am working on amyloid aggregation.So I take 5 Abeta-16-22 residue peptide to show amyloid aggregation.In this case I have got different result when I am using iwrap=1 or not.My input files are :  4000ps MD   NPT simulation
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  iwrap= 1,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  ig  =-1,
  cut = 10.0, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 2000000, dt = 0.002,
  ntpr = 2000, ntwx = 2000, ntwr = 2000
 /

And Another is :4000ps MD   NPT simulation
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  ig  =-1,
  cut = 10.0, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 2000000, dt = 0.002,
  ntpr = 2000, ntwx = 2000, ntwr = 2000
 /

When I use iwrap=1 from the starting of production run, in secondary structure analysis I don't get any extended Beta sheet .But when I don't use iwrap(after 72 ns I have to use iwrap=1 to run the simulation more) I get extended beta sheet.I have attached my secondary structure analysis.
Please help me out .
Thanks and regardsSaikat



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

use-1wrap_1.png
(image/png attachment: use-1wrap_1.png)

use-iwrap_0.png
(image/png attachment: use-iwrap_0.png)

Received on Fri Sep 01 2017 - 05:00:03 PDT
Custom Search