SQUEEZE: The optimal solution for molecular simulations
SQUEEZE is a method to reduce the computational cost of simulations of macromolecules performed under periodic boundary conditions. SQUEEZing allows removing the superfluous solvent molecules, by using the shape of the solute as the basis for the unit cell. This unit cell follows from the optimal packing of the solute, which takes only a few minutes to calculate. The reduction in volume is 50% on average, with respect to a rhombic dodecahedron, depending on the shape of the solute. For near spherical solutes the gain is less, while for some molecules the decrease in volume may be as much as 80%.
SQUEEZE comes in two flavours, SQUEEZE-E and SQUEEZE-B.

After submitting your structure, please wait a few minutes for your results
SQUEEZE-E is the general method, that allows setting up simulation systems for macromolecule, or for Ensembles that provide estimates for ranges of conformations.
Input structure or trajectory file (file may contain one or more structures)
Trajectory file
Format of the trajectory
Reference structure,
Not required for GRO, G96 or PDB structures: if no other file is provided, the first frame/structure will be used for reference
File may contain one or more structures, only the first one is used
Topology file
Format of the topology
Output format of the simulation box
Distance between periodic images (nm)
SQUEEZE-B (Bicone) is a special purpose adaptation that allows setting up an optimal system for protein folding simulations, starting from an extended strand. It uses a Bicone as the basis for the simulation cell.
Extended protein
Protein sequence
Please provide the protein sequence in one-letter format (e.g.LALAWKDEL)
Protein structure
Or: upload a PDB of the protein, the sequence will be extracted