Na ions got into the catalytic site during Production Run

From: Ching Wong (wongcw_at_TITAN.SFASU.EDU)
Date: Sun Nov 20 2005 - 17:34:01 CST

Hi. I am just a beginner. Please help. :)

My protein is negatively charged and I added eleven Na ions to zero out
the charges prior to energy minimization. Then I realize 3 Na ions got
into the catalytic site during the produciton run. I checked back with
the dcd files during the earlier energy minimization runs, one Na ion
already got in there. Then I restart the whole thing by fixing the
positions of all the Na ions (total 11) during the energy minimization
stage, then I proceed on production run. Again one Na ions got in the
catalytic site. My questions are

1.) is that okay to fix the Na ions during energy minimization?
2.) the Na ion got into the catalytic site again, should that be taken
into account when interpreting the rmsf result?
3.) My bigger problem is: the production run (with Na fixed during
energy minimization) actually crashed. (i got enough frames to realize
Na ion already got into the catalytic site). I wasn't able to use the
vel or xsc files from the previous Heating and equilibrium run. (I
could use that for my production run when I didn't fix the Na ions
during prep) The error shown in the log file is :
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

My conf file:
My cellBasisVectors are {68, 68, 82}
PMEGridSize are {80,80,80}

dcd minmax
frame 0 {33, 33, 40}
frame 489 {36.7, 36.7, 32.9}

4) My other doubt is how to set the cellBasisVector. I realize the cell
got bigger after waterMD (600K). It got smaller during production run.
So, how to set up the right CellBasisVectors? Do you think if that's
the reason my Production run crashed?

Thanks in advance for helping to solve these problems.



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