The best answer possible is the last part of what you pasted. Can you ask a specific question addressing that text?
Bill
<div>-------- Original message --------</div><div>From: Saman Yousuf ali <saman.yousufali64.yahoo.com> </div><div>Date:11/22/2016 9:31 PM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: [AMBER] simulation running error. </div><div>
</div>Dear All,Can anyone explains to me the following error,
| PMEMD implementation of SANDER, Release 14
| Run on 11/23/2016 at 04:51:25
| Executable path: /usr/local/amber14/bin/pmemd.MPI
| Working directory: /home/zuh/Working/sya/4cm6A-chain_apo
| Hostname: node15
[-O]verwriting output
File Assignments:
| MDIN: md_simulation.in
| MDOUT: md_simulation42.out
| INPCRD: md_simulation41.rst
| PARM: 4cm6A-chain_apo.prmtop
| RESTRT: md_simulation42.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: md_simulation42.mden
| MDCRD: md_simulation42.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
| MDFRC: mdfrc
Here is the input file:
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 1000, ntwx = 500, ntwr = 1000
/
| ERROR: I could not understand line 3269
-151.5212991 -24.8483053 546.3965801************-142.8141370-245.7454655
*s in the inpcrd file often indicate an overflow of the Fortran format used
to store coordinates in the inpcrd/restart files. This often happens when
coordinates are not wrapped into the center cell (when iwrap = 0) and some
particles diffuse too far away. Try restarting from your last good restart
file and setting iwrap=1 or using a NetCDF restart file format. See the
Amber manual for details
Best Regards, Saman Yousuf Ali
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Received on Tue Nov 22 2016 - 22:00:04 PST
