On Tue, 2014-02-25 at 09:58 +0000, Mele N. wrote:
> Thanks a lot to take time to answer.
>
> I kept equilibration because I just copy past the same file and change parameter and forgot to change the name at the beginning by "heating".
> Actually my heating step doesn't work. It crashed at the beginning:
>
> vlimit exceeded for step 0; vmax = 54.5176
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 35579 45871 45873
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I had a look on my packmol input file and output file and I created a cubic box:
> This is my input file:
>
> tolerance 2.0
>
> filetype pdb
>
> output box_mix.pdb
>
> structure WATER.pdb
> number 2684
> inside box 0. 0. 0. 90. 90. 90.
> end structure
>
> structure dmso.pdb
> number 5560
> inside box 0. 0. 0. 90. 90. 90.
> end structure
>
> And this is the input file from leap:
>
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberparams tripos1.frcmod
> loadoff tripos1.lib
> MOL = loadpdb box_mix.pdb
> setbox MOL vdw
> saveamberparm MOL mix.prmtop mix.inpcrd
> savepdb MOL box_leap.pdb
> quit
>
> Am I wrong in the way to build my box?
I don't know. If you know the experimental density of a 2:1 DMSO-water,
mixture you should be able to compute whether a 90x90x90 box is big
enough.
When I quickly calculated how many water molecules were necessary to
fill a 90x90x90 A box to achieve a density of 1 g/mL, I got ~24000 water
molecules (which is far fewer than the 2684 water molecules plus 5560
DMSO molecules you added). Have you visualized your system?
I strongly encourage you to use the "checkoverlap" command in cpptraj to
see if you have overlapping solvent molecules. It's also always helpful
to visualize your system and see if you can find any obvious problems.
This looks to me like you have steric clashes so strong that not even
minimizations can solve it.
You can look at the maximum gradient printed at the end of your
minimization output file to see where clashes might be occurring. I
still think there is a problem with your box definition leading to the
clashes. Check that the resulting volume you get by multiplying the box
edge lengths matches what you expect based on your packmol input.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 05:00:03 PST
