Dear Jason
If iwrap= 1, the coordinates written to the restart and trajectory files will be "wrapped" into a primary box. This means that for each molecule, its periodic image closest to the middle of the "primary box" (with x coordinates between 0 and a, y coordinates between 0 and b, and z coordinates between 0 and c) will be the one written to the output file.
So, in my system(protein in solution), while ti is performing, the system is not wrapped anymore!
(iwrap=1) in my input.
Best
morteza
________________________________
From: Khabiri, Morteza
Sent: Thursday, October 15, 2015 9:18 AM
To: amber.ambermd.org
Subject: System gets unwrap while iwrap=1 in ti
Dear amber user
I am doing ti calculation with amber14 and pmemd. I dont know why the system gets unwrap during ti calculation while the iwrap is 1. my input is as follow:
runti
&cntrl
imin = 0, nstlim = 15000, irest = 1, ntx = 5, dt = 0.002,
ntt = 3, temp0 = 298.0, gamma_ln = 5.0,
ntc = 2, ntf = 1, ntb = 1, ntp = 0,
ioutfm = 1, iwrap = 1, ntxo = 2,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 1000,
icfe = 1, clambda = 0, idecomp=0,
timask1 = ':116,149', timask2 = ':159,160',
ifsc=1, logdvdl=1, dynlmb=0.0001, ntave=15,
scmask1 = ':116,149', scmask2 = ':159,160'
&ewald
/
best
Morteza
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Received on Thu Oct 15 2015 - 07:30:03 PDT
