Date: Tue, 14 Feb 2017 05:37:46 +0000 (UTC)
Dear All,I have run 50 ns simulation of hoodimeric protein using amber14 PMEMD.MPI. Each chain is in complex with cofactor NADPH and ligand. MD production input file is pasted below,
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
/
After 26ns, I got error and job killed,| 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.
then I added iwrap=1 flag and rerun siumlation using 26 rst file. When job finished, I reimaged mdcrd files using autoimage keyword and plotted rmsd as well. Upon loading reimaged trajectories into VMD, I observed that both subunitsdisplaced from their starting positon. After 8ns rmsd of dimer complex jumps from 5 to 25 angstroms. Please help me in this regards.
Thanks
BestSaman Yousuf Ali
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(image/png attachment: 4cm6_ADchain-complex-rmsd-dimer.png)
