RE: Na ions got into the catalytic site during Production Run

From: Michel Espinoza-Fonseca (
Date: Mon Nov 21 2005 - 10:16:38 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
You can just simply tell VMD to add the ions to increase the minimal distance between them and your protein (e.g., 10 A) by typing:
autoionize -psf your_protein.psf -pdb your_protein.pdb -is your_desired_conc -o your_protein -from 10

> 1.) is that okay to fix the Na ions during energy minimization?

you can fix your ions as well, but usually you can leave them free and you won't encounter any problem.

> 2.) the Na ion got into the catalytic site again, should that be taken
> into account when interpreting the rmsf result?

Your ions should not reach the catalytic site unless you have added them to that site.

> 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.

Unless you're using a protein-membrane system, I strongly suggest you to disable the FlexibleCell option. In addition, you can increase the margin to 10 A (or whatever fits well to your system) during the equilibration process, and then reduce it for your actual production runs.

> 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?

Try to check any of the NAMD tutorials available online. You'll find helpful information on how to setup your systems and how to perform both equilibration and production runs.

> Thanks in advance for helping to solve these problems.

No problem, good luck!



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