How to calculate PBC box size while doing protein unfolding MD simulation

National Centre for Biological Sciences (NCBS-TIFR)

Thank you very much, I have changed the thickness value to 15 and now my simulation works fine. Thank you very much.

National Institute of Physics

You should determine the water box sizes based on the protein unfolded structure, using for example one of the unfolded configurations. Based on this unfolded structure, you can determine (x_max, x_min), (y_max, y_min) and (z_max,z_min) of protein. Then, construct a water layer around the protein with thickness at least the cutoff of non-bonded interactions size: let's say if the cutoff=11-12 Angstrom, then the thickness of the layer is 15 Angstrom (assuming that the water box may shrink a little if the water box is not initially equilibrated at normal conditions, i.e., density = 1 gr/cm^3). Then, the big water box sizes are defined as:

big_sizeX = x_max-x_min + 2*thickness

big_sizeY = y_max-y_min + 2*thickness

big_sizeZ = z_max-z_min + 2*thickness

Then, after building a water box with these dimensions (big_sizeX, big_sizeY, big_sizeZ), you can solvate the folded protein structure in this 'big' water box. With this, then, you are sure that even if the protein gets unfolded, the images will not see each other.

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National Institute of Physics

big_sizeX = x_max-x_min + 2*thickness

big_sizeY = y_max-y_min + 2*thickness

big_sizeZ = z_max-z_min + 2*thickness

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National Centre for Biological Sciences (NCBS-TIFR)

Thank you Hiqmet Kamberaj.

But where do I get this information from? How can I determine (x_max, x_min), (y_max, y_min) and (z_max,z_min) of protein from trajectory files?

National Institute of Physics

You can use vmd, for example, with command 'measure minmax' in TkConsole.

National Centre for Biological Sciences (NCBS-TIFR)

Thank you very much.

I calculated minmax using VMD as you suggested and calculated big_sizeX, big_sizeY and big_sizeZ taking the thickness of 10. How do I correlate these values to size of the cubic box (-d option) I need to use in the following command:

gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic

National Institute of Physics

Thickness 10 angstrom with a cutoff of at least 10 angstrom (as usually suggested for biomolecular systems) is a little small. It is recommended that the thickness should be greater than cutoff of non-bonded interactions. As I said in the previous post, first,

big_sizeX = x_max-x_min + 2*thickness

big_sizeY = y_max-y_min + 2*thickness

big_sizeZ = z_max-z_min + 2*thickness

then,

d = max(big_sizeX, big_sizeY, big_sizeZ)

where (x_min,x_max,y_min,y_max,z_min,z_max) are calculated using the most unfolded protein structure that you may have to see during the simulations.

National Centre for Biological Sciences (NCBS-TIFR)

Thank you very much, I have changed the thickness value to 15 and now my simulation works fine. Thank you very much.

How to measure correctly the cell dimensions by using the measure minmax command in VMD?

Recently, I have been running a MD simulation however I got the error "Periodic cell has became too small for orginal patch grid" and this mesagge could be related to the incorrect measurement of the cell dimensions by using the following commands in VMD:

8 answers

Asked 6th Aug, 2018

Marlet Martínez-Archundia

Dear all,

set all [atomselect top all]

measure center $all

measure minmax $all

From this last point, one can gets (x1, y1, z1) (x2,y2,z2). However what is the correct way to obtain the cell dimensions (box size) for periodic boundary conditions?

Thanks in advance and best regards,

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During MD simulation, tetrameric protein diffuses in the simulation box and ends up crossing the periodic boundaries. One of four chains is jumping to the other side of the simulation box. For my analysis, I need all chains together and centered.

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Asked 19th Feb, 2016

Tugba Ozturk

I tried to use pbc wrap in VMD. But after wrapping the trajectory file, some of atoms are being transformed in an awkward way so I end up seeing stretches while visualizing the protein in new cartoons mode. I am guessing it's because of center of mass of my selection moving significantly.

The command I have used:

pbc wrap -center com -centersel "protein" -compound residue -all

I could not find a way to fix that, somebody else reported a similar problem in vmd mailing list, so far no replies.

Any suggestions?

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Nadim Ferdous

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I used "draw delete all" command to delete the pbc box in VMD, but it's just removed from the current frame. How can I remove it from all frames?

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Asked 7th Feb, 2019

Dariush Mohammadyani

Is box size 1nm for Molecular dynamics simulation in Gromacs is inappropriate?

For molecular dynamics simulation using Gromacs 5, the solvation box size is 1nm according to gromacs manual. Is it inappropriate? or depends with the protein size ?

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Asked 29th Jun, 2022

Tanusree Mookherjee

Solvating a system using namd and vmd, with desired water box dimension and desired number of water molecules?

How can I create a water box around our system with desired dimensions with desired number of solvent molecules around it (say a 50A x 50A x 50A cubic box containing 1000 water moleclues.) using namd and vmd ?

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Asked 27th Jul, 2021

Krithika Unmesh

I came across the following command:

package require solvate

solvate abc.psf abc.pdb -t 5 -o abc_wb

But, what does the flag, -t 5 mean here ? What distance does 5 represent? And also, is there a way to set the number of solvent molecules? Can anyone help me out.

Thanks in advance.

How could I select a range of ATOMS by using VMD Program?

I have been searching in the web and VMD Tutorials how to select a range of atoms by using VMD however I have just found only how to select a range of residues for example residue: resid 13 to 15

12 answers

Asked 25th Sep, 2018

Marlet Martínez-Archundia

Dear all,

However I have not found information about selecting a range of atoms eg. atoms 1340-1642 of my protein. I am interested to do this due to the numbering of my chain, in which residues numbers are repeteated but not atoms.Thus, I am interested to select only a range of atoms.

Does anyone have any suggestion?

Thanks in advance and best regards

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How to solve Amber Leap PDB preparation error "atom does not have a type"?