normal hole in the simulation box

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3 months 3 weeks ago #7344 by edesantis
edesantis created the topic: hole in the simulation box
Hi Martini users,

i am trying to simulate a crystal supershell (5x5x5 unit cells) with martini ff in gromacs 5.

I build the system in aa representation, then I converted it in CG using the martinize.py scritp,

following the tutorial, I've done a brief equilibration in water, the after the solvatation of the system with non-polarizable water, I've perform another energy minimization followed by the equilibration.

then I've performed md simulation in the NVT ensemble,

It happened that during the first steps of md, an empty (no protein no water) hole was created in my simulation box. during the md simulation the hole size became bigger

I've tried to calculate forces using different algorithms but the hole is formated every time,


do you have an idea of the reason why I found this hole? do you have any suggestion to avoid its formation??


thank you in advance,
regards
Emiliano De Santis

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3 months 3 weeks ago #7345 by peterkroon
peterkroon replied the topic: hole in the simulation box
Hi,

this is probably because in your solvation step the computer couldn't get enough waters in your box. Try doing a NPT equilibration from the start, or resolvate the result of your NVT simulation (and repeat). You may want to restrain the positions of your proteins, but that's up to you.

Peter

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3 months 3 weeks ago #7346 by edesantis
edesantis replied the topic: hole in the simulation box
Hi Peter,
thank you for your quick answer,

I'd prefer to avoid NPT ensemble since a dynamic volume of the box could alter the reticolar parameter of my crystal,

in your opinion is it possible to force in the solvation step to put more water inside the box?
in gmx genbox tool (gromacs 4) there were the flag -try, that allows to try several times the addition of water molecules to fill the eventual holes created, but it seems to be not present anymore in the gmx solvate version, do you know how to do it?
changing the van der Waals radii (-radius, the equivalent of the old flag -vdvw of gma genbox) could be a good strategy for you?
this value now is set to 0,21 (as suggested in the tutorial)

sorry for the many question, but I am quite a beginner of Martini ff....

thank you in advance
regards,
Emiliano

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3 months 3 weeks ago #7347 by peterkroon
peterkroon replied the topic: hole in the simulation box
Ok. How about position restraints during a NPT equilibration? Would that work?
Yes, it is possible to convince gromacs to put more particles in your box. -try won't help too much in my experience. You're better of shrinking the vdw radius by either using -radius, or making an applicable vdwradii.dat (see <gromacs-dir>/share/gromacs/top/vdwradii.dat).
Either way, you may need to do several iterations of solvating+equilibrating...
Or try to solvate using a pre-equilibrated waterbox (should be on this site somewhere)

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3 months 3 weeks ago #7348 by edesantis
edesantis replied the topic: hole in the simulation box
Hi Peter,

so you suggest to put the flag -DPOSRES in the NPT dynamics, do I understand well?

in this case the positions of the atoms belonging to the protein would be maintained fixed??

in my solvation step I've used the water-box-CG-303K-1bar.gro, that should be the equilibrated water box that you mentioned....
I've also tried to solvate again the pre-equilibrated box (containing both the protein and the water) and after a while the hole is formed anyway (in this case the density of the system, computed total_mass/volume, was 1.4 the experimental one)

regarding -radius flag, in your opinion, witch value could be a good choice?


thank you again for your help
Emiliano

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3 months 3 weeks ago #7349 by peterkroon
peterkroon replied the topic: hole in the simulation box
Yes, but there may be some artefacts (i.e. the reference positions get rescaled by the changing box) so read the documentation carefully.

I've also tried to solvate again the pre-equilibrated box (containing both the protein and the water) and after a while the hole is formed anyway (in this case the density of the system, computed total_mass/volume, was 1.4 the experimental one)

So take that outcome, solvate, and equilibrate again and keep doing that untill the problem is solved.

regarding -radius flag, in your opinion, witch value could be a good choice?


I don't have a number at hand. Try with just a water box in NPT to see at what number the box size is stable.

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3 months 3 weeks ago #7350 by edesantis
edesantis replied the topic: hole in the simulation box
ok,
I will follow your suggestions...


thank you again
Emiliano

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3 months 2 weeks ago #7353 by edesantis
edesantis replied the topic: hole in the simulation box
I've tuned the gmx solvate -radius parameter until I achieved the stability of the box dimensions in the NPT ensemble, now it seems that everything is working well...

thanks again,

regards,
Emiliano

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