Dear Bill,You are right in last line it is suggested that either i use iwrap =1 flage or use netcdf restart. I have added iwrap =1 flag in my simulation input file and it starts running but now my question is should i restart my simulation again or it it is fine to continue from last file which is 40 ns. Best Regards, Saman Yousuf AliJunior Research Fellow,
On Wednesday, November 23, 2016 10:55 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
The best answer possible is the last part of what you pasted. Can you ask a specific question addressing that text?
Bill
-------- Original message --------From: Saman Yousuf ali Date:11/22/2016 9:31 PM (GMT-08:00) To: AMBER Mailing List Subject: [AMBER] simulation running error.
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 - 22:30:02 PST
