Dear Martis,
Thanks for your prompt response. My job stopped at 40 ns. After adding iwrap=1 flag. I restart whole simulation or from last file? Best Regards, Saman Yousuf Ali
On Wednesday, November 23, 2016 10:42 AM, Elvis Martis <elvis_bcp.elvismartis.in> wrote:
Hi,Please add iwrap=1 flag and rerun your simulations.
Regards
|
Elvis Martis Ph.D. Student, Bombay College of Pharmacy |
| | Email: elvis_bcp.elvismartis.in
Website:
http://www.elvismartis.in
group website:
http://www.profeccoutinho.net.in/
Address: Kalina, Santa Cruz [E], Mumbai, 400 098, INDIA
Alt. e-mail: emartis12.live.com
|
On 23 November 2016 at 11:01, Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
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 - 22:00:03 PST
