Hello,
I am currently running short equilibration jobs that fail with the error
'Nonbond cells need to be recalculated'. The archive post '
http://archive.ambermd.org/201306/0428.html' suggests that the initial
water box dimension estimate (that I supplied to chamber based on an
estimate in VMD) was too generous . Indeed the box shrank about 1A per side
from my initial estimate (comparing 06md.restrt versus inpcrd2 below).
However, I'm still getting the same error though the change in box size
from the last successful run is now < 0.01 A.
$ tail 06md.restrt inpcrd2
==> 06md.restrt <==
.............
-0.3765108 0.1185375 0.1430280 -0.1165733 -0.0713152 -0.2362562
0.0538754 -0.1661195 -0.1460433 0.1523594 -0.0445150 0.1817211
-0.1523692 0.2286251 0.0191365 0.2526394 -0.0780730 0.0021221
0.0259425 0.0574392 0.0234660
72.8648615 72.5771613 73.0273340 90.0000000 90.0000000 90.0000000
==> inpcrd2 <==
.............
30.0898000 2.6241800 -6.3353300 6.7333500 -26.6361000 11.2759000
-16.3569000 22.4362000 -24.8006000
72.8695172 72.5817986 73.0320000 90.0000000 90.0000000 90.0000000
Am I missing something obvious? Attached is my input file, but I put the
rest of the stuff on dropbox:
10md.in: production (500000 = 1ns)
&cntrl
imin = 0, ntx = 5, irest = 1, nstlim = 50000,
temp0 = 298.15, tempi = 298.15, ig = 71287,
ntc = 2, ntf = 1, ntt = 1, dt = 0.001,
ntb = 2, ntp = 1, tautp = 1.0, taup = 1.0,
ntwx =1000, ntwe = 0, ntwr = 1000, ntpr =1000,
iwrap = 1,
ntr = 1, nscm = 100,
restraintmask = ':1-109', restraint_wt = 0.5,
/
$AMBERHOME/bin/pmemd.cuda -O -i 07md.inp -o 07md.out -p prmtop -c
06md.restrt -ref inpcrd2 -r 07md.restrt
https://www.dropbox.com/s/irxkms9861ne9qc/seriesoftubes.tgz
Thanks in advance for the help
Pete
--
======================
Peter Kekenes-Huskey, Ph.D.
Postdoctoral Researcher
UCSD Dept of Pharmacology
4205 Urey Hall
9500 Gilman Avenue
La Jolla, CA 92093
http://mccammon.ucsd.edu/~huskeypm/
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Received on Thu Mar 27 2014 - 22:00:03 PDT
