Hi,
Please add iwrap=1 flag and rerun your simulations.
Regards
*Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
[image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
Website: http://www.elvismartis.in <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
<
https://in.linkedin.com/in/elvisadrianmartis>
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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>
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Received on Tue Nov 22 2016 - 22:00:03 PST
