• Solvents: Select the solvent model to employed: Implicit or Explicit
  • Implicit Solvent: An implicit solvent model is a simulation technique that eliminates the need for explicit water atoms by including many of the effects of solvent in the inter-atomic force calculation. The elimination of explicit water accelerates conformational explorations and increases simulation speed at the cost of not modeling the solvent as accurately as explicit models. QwikMD uses the Generalized Born Implicit Solvent implemented in NAMD.
  • Explicit Solvent: QwikMD uses VMD solvate plugin to generate a cubic box centered in the geometrical center of the system and box's edge is calculated by:

    MD Protocol box : box_{edge} = (\sqrt{x^2+y^2+z^2}) + 15

    SMD Protocol box : box_{x} = box_{y} = (\sqrt{x^2+y^2}) + 15 | box_{z} = z + PullingDistance + 15 .

    , where x,y and z are the dimensions of structure in the three axis. Box dimensions in Å. When preparing the simulation, the simulation is translated to the origin {0,0,0}.

    Note: The water box created by QwikMD is somewhat big for most studies. The big water box was adopted as a safety measure. Ideally, one should work with a box, which is large enough that the protein does not interact with its image in the next cell if periodic boundary conditions are used. The use of periodic boundary conditions involves surrounding the system under study with identical virtual unit cells. The atoms in the surrounding virtual systems interact with atoms in the real system. These modeling conditions are effective in eliminating surface interaction of the water molecules. As the standard water model for CHARMM, TIP3P is the model employed in the simulations prepared with QwikMD.

• Salt Concentration: Ions should be placed in the water to represent a more typical biological environment. They are especially necessary if the protein being studied carries an excess charge. In that case, the number of ions should be chosen to make the system neutral. One must set the desired salt concentration. The default Salt Concentration is 0.15 mol/L. QwikMD uses VMD autoionize plugin to place the ions and even if the Salt Concentration is set to ZERO, ions will be added to neutralize the total charge of the system. In the case of the Generalized Born implicit solvent, the salt concentration is used as ion concentration parameter value (see Generalized Born Implicit Solvent Configuration Parameters).
• Choose Salt: Salt ion pairs currently available are NaCl and KCl.

• Molecular Dynamics Simulations : Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules in the context of N-body simulation. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms. In the most common version, the trajectories of atoms and molecules are determined by numerically solving the Newtons equations of motion for a system of interacting particles, where forces between the particles and potential energy are defined by interatomic potentials or molecular mechanics force fields.

  Note : When running MD simulations it is very important to run more than one replica of the same system. Long trajectories usually also helps one to sample different conformations. Therefore a long simulation is important if big conformational changes are expected. If you want to learn more about sampling and molecular dynamics check the link at the bottom of this window.

• Steered Molecular Dynamics Simulations : Steered molecular dynamics (SMD) simulations, or force probe simulations, apply forces to a protein in order to manipulate its structure by pulling it along desired degrees of freedom. These experiments can be used to reveal structural changes in a protein at the atomic level. SMD is often used to simulate events such as mechanical unfolding or stretching.

  There are two typical protocols of SMD: one in which pulling velocity is held constant and one in which applied force is constant. Typically, part of the studied system (e.g. an amino acid in a protein) is restrained by a harmonic potential. Forces are then applied to specific atoms at either a constant velocity or a constant force in the direction of the pulling axis. QwikMD is set to perform constant velocity SMD.

  The pulling axis is defined by the vector formed by the centers of the selections Anchoring and Pulling Residues. During the system preparation phase, the initial structure pulling axis is aligned with the z-axis and the pulling speed vector assumes only the z component.

• Equilibration step: This protocol step is composed by 1000 steps of Energy Minimization, a "Temperature Ramp", where the temperature in raised from 60 K to the chosen "Temperature", 1 K/ρs and 1.0 ns of MD simulation. During the equilibration step, the backbone atoms of protein and nucleic residue are restrained in space.

Default Configurations

• Integration Step: The time step used in any MD simulation should be dictated by the fastest process (i.e. movement of atoms) taking place in the system. Among the various interactions, bond stretching and angle bending are the fastest, with typical bond stretching vibrations occurring on the order of once every 10-100 femtoseconds. Using a time step of 2 fs, which is close to the vibrational period (10 fs) of linear bonds involving hydrogen (fastest vibrations, since hydrogen has small mass), requires that these bonds be fixed, and only slower vibrations may be free to move, such as dihedral angle bending. For large molecules, these slower vibrations typically govern the behavior of the molecule more than the quicker ones, so bond fixing is somewhat acceptable, but should be avoided for accurate simulations. One prefers to use an MD timestep which is ~ 1/10 of the fastest interactions in the simulation. For simulations with time step of 1 fs, one should use rigidBonds for water because water molecules have been parametrized as rigid molecules. QwikMD adopts 2 fs time step as standard.

• NPT Ensemble : In the isothermal-isobaric ensemble (NPT), number of atoms (N), pressure (P) and temperature (T) are conserved. To do control pressure and temperature a thermostat and a barostat are needed. The NPT ensemble corresponds most closely to laboratory conditions with a flask open to ambient temperature and pressure. Langevin dynamics is a means of controlling the kinetic energy of the system, and thus, controlling the system temperature and/or pressure. QwikMD uses standard NAMD protocols that employ Langevin dynamics.

• Solvent: Select the solvent model to employed: Vacuum, Implicit or Explicit
  • Vacuum: Absence of solvent and commonly know as simulation in gas phase. Non-bonded interactions cutoff distances are updated to: cutoff: 16 Å, switchdist: 15 Å, pairlistdist: 18 Å. When selected, QwikMD also applies a dielectric constant of 80.0.
  • Implicit Solvent: QwikMD uses the Generalized Born Implicit Solvent implemented in NAMD. Non-bonded interactions cutoff distances are updated to: cutoff: 16 Å, switchdist: 15 Å, pairlistdist: 18 Å and an alphaCutoff: 18 Å is used. A solventDielectric: 80 Å is used to represent water as solvent.
  • Explicit Solvent: QwikMD uses VMD solvate plugin to generate a water box centered in the geometrical center of the system and box's edge is calculated by:

    MD/MDFF Protocol box : box_{edge} = (\sqrt{x^2+y^2+z^2}) + 2 * Buffer

    SMD Protocol box : box_{x} = box_{y} = (\sqrt{x^2+y^2}) + 2 * Buffer | box_{z} = z + PullingDistance + 2 * Buffer .

    , where x,y and z are the dimensions of structure in the three axis ("Minimal Box" option off). Box dimensions in Å. When preparing the simulation, the simulation cell is translated to the origin {0,0,0} except in "MDFF" protocol.

    Note: The water box created by QwikMD is somewhat big for most studies. The big water box was adopted as a safety measure. Ideally, one should work with a box, which is large enough that the protein does not interact with its image in the next cell if periodic boundary conditions are used. The use of periodic boundary conditions involves surrounding the system under study with identical virtual unit cells. The atoms in the surrounding virtual systems interact with atoms in the real system. These modeling conditions are effective in eliminating surface interaction of the water molecules. As the standard water model for CHARMM, TIP3P is the model employed in the simulations prepared with QwikMD.

• Minimal Box: Rotate the system and apply a simple solvent box padding distance, instead of the formula described in the "MD/MDFF Protocol box" description. The usage of this option should be used carefully and the "Buffer" distance should be increased to account system rotation/tumble during the simulation (see VMD solvate plugin).
• Salt Concentration: Ions should be placed in the water to represent a more typical biological environment. They are especially necessary if the protein being studied carries an excess charge. In that case, the number of ions should be chosen to make the system neutral. One must set the desired salt concentration. The default Salt Concentration is 0.15 mol/L. QwikMD uses VMD autoionize plugin to place the ions and even if the Salt Concentration is set to ZERO, ions will be added to neutralize the total charge of the system. In the case of the Generalized Born implicit solvent, the salt concentration is used as ion concentration parameter value (see Generalized Born Implicit Solvent Configuration Parameters).
• Choose Salt: Salt ion pairs currently available are NaCl and KCl.

• Molecular Dynamics Flexible Fitting: the Molecular Dynamics Flexible Fitting (MDFF) method can be used to flexibly fit atomic structures into density maps, specially cryo-electron microscopy (cryo-EM) maps. cryo-EM can capture large macromolecular complexes at different functional states usually inaccessible to X-ray crystallography techniques. However, the resolution of these maps are considerable lower when compared to the X-ray structures. Combine both structural data from different sources and resolutions allow the user to have a high resolution atomic structure representing the conformational state captured on the cryo-EM map.

  Note : Despite of preparing the system with QwikMD, the user is redirected to the MDFF GUI to set up, perform and analyze the simulation.

• Residues Table: The Residues Table is main component of the "Structure Manipulation/Check" window and lists all the residues included in the selection made on "Chain/Type Selection" menu. The residues are listed in the same order as in the "Main Table", which is the order the residues are listed in the initial structure file. To facilitate the browsing through the residues list, one can change the sort criteria and sort the table by a specific column pressing the columns header.

  Residues Marked in Red: When the residue is not recognized by QwikMD, meaning that the specific residue name doesn't match the residue names contained in the Topology files loaded by QwikMD. One must add the stream file containing the topology and the parameters, rename, change the residue type or delete the residue.

• Table Options: The action triggered when a residue is selected on the Residues Table is determined by the table option selected. One should always select the table option first and then the residue(s) to be manipulated/visualized.
• Mutate: Mark one residue to be mutated during the structure preparation phase. The mutations are only available for protein and nucleic residues and are dependent on the residue type, for instance, a protein residue can only be mutated to another protein residue.

WARNING: Even a very small number of mutations may affect the structure of a protein drastically. Be very careful when using the mutation tool of QwikMD as you might create artifacts in your simulation.

• Prot. State: Mark one residue to assign a protonation state during the structure preparation phase. Amino acids, depending on their environment, can present different protonation states. It is recommended to check the protonation state of the amino acids before an MD simulation. Several tools can be used for that. One of the most popular tools is the PROPKA Server. The assignment of protonation states is only available for protein residues and the options available are dependent on the residue selected, e.g., only two options are available for the aspartic acid (ASP), neutral (ASP) or protonated (ASPP) state.

Histidine Residues: Of the 20 amino acids, histidine is the only one that ionizes within the physiological pH range ~7.4. This effect is characterized by the pKa of the amino acid side chain. For histidine, the value is 6.04. This leads to the possibility of different protonation states for histidine residues in a protein, and makes the consideration of the proper state important in MD simulations. The viable states are one in which the delta nitrogen of histidine is protonated - listed with residue name HSD - one in which the epsilon nitrogen of histidine is protonated - HSE - and one in which both nitrogens are protonated - HSP. If not set by the user, QwikMD uses HSD as the standard histidine protonation state.

• Add: Add residue(s) previously marked to be deleted.
• Delete: Mark residue(s) to be deleted during the preparation phase.
• View: Disable all manipulation options and only represent the selected residue(s).
• Rename: Change the residue name to match the residue names in the CHARMM forcefield topology files. The possibilities available to rename the selected residue are dependent on the residue type, such as a protein residue can only be renamed to a residue categorized as a protein residue. If the proper residue name is not available, one must add the correspondent Topology+ParameterFiles.str, change the residue type and further rename or delete the residue.

WARNING: The structure preparation phase cannot start while the system contains unrecognized residues.

• Type: Sometimes, molecules categorization can be misleading (or even nonexistent), which hinders the correct identification of residues. For instance, if the user intends to mutate the nucleotide Adenosine Triphosphate (ATP) by another nucleotide, it would be possible to mutate to a Guanine, Adenine, Cytosine or Thymine (or Uracil in RNA), as they share the same category as nucleic residues (nucleic). To avoid such structural errors, QwikMD gives the possibility to change residues type (category), so a logical choice can be made.
• Edit Atoms: Residues fine grained edition, where one can change the residue number (resid), the atom's name and delete one or more atoms. Taking the example of the acetate residues in the HIV-1 protease structure (pdb entry 1KJF). The residue name in the original pdb structure is ACT and is marked as unrecognized by QwikMD since the same residue is named as ACET in the CHARMM topology file. In this case, one must change the residue name from ACT to ACET, which raises another topological issue, where none of the atoms name in the pdb match the atoms name the topology. In this case, one must rename also the atoms. For reference purpose, the topology entry and a numbered molecular representation of the residue is given to user.

• Apply/Edit button: Apply residues selection during the SMD Anchoring/Pulling residues selection or open the "Edit Atoms" window when the "Edit Atoms" option is selected.
• Clear Selection: Deselect the current selected residues.

• Default Topology files:
  • top_all36_carb.rtf, top_all36_cgenff.rtf, top_all36_hybrid.inp, top_all36_lipid.rtf, top_all36_na.rtf, top_all36_prot.rtf
• Default Stream files:
  • toppar_all36_carb_glycopeptide.str, toppar_water_ions_namd.str
• Default Parameters files:
  par_all36_carb.prm, par_all36_cgenff.prm, par_all36_lipid.prm, par_all36_na.prm, par_all36_prot.prm

• Residue NAME: name to be displayed in QwikMD residues list. Protein and nucleic residues must have the same "Residue NAME" and "CHARMM NAME", while hetero, glycan and user defined residue types can assume different residues names, such as, the acetate ion residue: "Residue NAME"=Acetate", "CHARMM NAME"= "ACET".
• CHARMM NAME: residue name in the CHARMM topology file. Note: Sometime the residues' name listed in the CHARMM topology files can be composed by more than 4 characters, which is a violation of the pdb file format. In this case, a warning message is prompted to the user and the correspondent line of the residue colored in red and one must rename the "CHARMM NAME" to a unique 4 letter residue name. The name of the residue is also updated in the file stored in the QwikMD library folder.
• Default Parameters files:
  par_all36_carb.prm, par_all36_cgenff.prm, par_all36_lipid.prm, par_all36_na.prm, par_all36_prot.prm
• Topo & PARM File: File containing the residues topology and parameters.

WARNING: After all the editions to the residue's list and before leaving the "Topology & Parameters Selection" window, one must press "Apply" and reset QwikMD gui by pressing the "Reset" button in one of the Run Tabs.

• Topologies & Parameters: Comparison between the residues' name in the initial structure and the residues' name in the CHARMM36 topology files. Once a mismatch is detected, the residue is marked in red in the "Residues Table" and the correspondent chain is colored as "Throb" in the "Main Table". The system preparation phase cannot start before this warning is solved.
• The easiest way to overcome the lack residue topologies and parameters is to delete the residue, which may not be desirable as the referred molecule might well be relevant. Thus, one has to provide QwikMD with the missing force field topology and parameters. If the topology and the parameters are available, i.e., in the literature, but not yet added to the force field, the user may add to QwikMD through Topology & Parameters Selection. These parameters can also be obtained from web servers, with varying levels of accuracy, such as CGenFF webserver. The most accurate and recommended method for furnishing missing parameters requires advanced knowledge, namely familiarity with the Force Field Tool Kit (FFTK) plugin in VMD. The ffTK plugin assists with the process of parameterization, employing quantum chemistry programs.
• Chiral Centers: Detection of cis chirality errors in protein and nucleic acid structures using the Chirality plugin in VMD. For more information how to fix chirality errors please follow the Structure Check tutorial.
• All amino acids but glycine have at least one chiral center at Cα. Threonine and isoleucine have an additional chiral center at Cβ. According to the D- / L- naming convention, naturally occurring amino acids are found in the L-configuration. Note, however, that D-amino acids do occur in biology, e. g., in cell walls of bacteria. Nucleic acids also have chiral centers. For example, in DNA the atoms C1', C3', and C4' are chiral, while RNA has an additional chiral center at C2'. Chirality is central to all molecular interactions in biological systems. A simple experiment demonstrates the principle: try to shake someone's left hand with your right.
• Cispetide Bond: Detection of cis peptide bonds in protein structures using the Cispeptide plugin in VMD. For more information how to convert fix chirality errors please follow the Structure Check tutorial.
• In naturally occurring proteins most peptide bonds are in the trans configuration. However, sometimes cis peptide bonds do occur. The vast majority of cis peptides is observed at a proline, Xaa-Pro, Xaa being any amino acid. But non-proline Xaa-non Pro cis bonds are also found in proteins, although they occur much less frequently than Xaa-Pro. The configuration of the peptide bond is central to the sort of secondary structure the protein backbone can adopt. It is easy to understand by imagining a normal α-helix and converting a trans peptide bond into its cis form. The result is that the hydrogen bond network stabilizing the helix is broken and the helix will be unstable in long simulation.
• Sequence Gap: Detection of non-consecutive numbering of the protein and nucleic residues within each chain. If the residues sequence present a gap, another test is performed to evaluate if the residues are bonded, avoiding false detection of pre-crystallization sequence deletions. Due to the complex structure of carbohydrates (glycan), this test is not performed for such molecule types.
• PDB Insertion Codes: Sometimes the initial structure presents insertion codes in the residues sequence. Rather than be numbered sequentially, some structures present residues numbering as 47, 47A, 47B and so on. This different numbering rises from the comparison between homologous proteins which have different chain lengths, and the authors who wants to preserve the reference among the different proteins use additional characters to identify non-matching residues between homologous sequences.
  QwikMD reorders the residues to avoid unintentional deletion of the residues presenting different insertion codes. During the loading process, the residues sequence is checked for the existence of insertion codes and new residues IDs are assigned to ensure sequential numbering. In the end of the check structure process, a warning message is prompted to the user followed by the reference table displaying the relationship between the initial and the new numbering sequence. The reference table is then saved in the "setup" folder, within the working directory during the preparation phase, in the file "Renumber_Residues.txt".
• Torsion Angles Outliers/Marginals: Evaluation of the distribution of the φ and ψ backbone angles. The percentage of angles consider as Outliers and Marginals are good indicators of the stereochecimal quality of the structure. QwikMD uses the command line of Torsion Plot VMD plugin to perform this evaluation. For more information, please visit the Ramaplot Plugin.

• Lipid: Membrane lipid composition. Only two types of lipid composition are currently available:
  • POPC: membrane 100% composed by 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylcholine
  • POPE: membrane 100% composed by 3-palmitoyl-2-oleoyl-D-glycero-1-Phosphatidylethanolamine
• x/y entries: membrane dimensions in the x-axis/y-axis in Å. The initial position of the membrane is assigned to the center of the system currently selected.
• Box: Draw the box where the membrane will be positioned.

  Note: Due to the slow process of building the membrane and to avoid rounding floating point arithmetic rounding errors generated during coordinates translation and rotation process, the position of the membrane is defined using a temporary box, and then the membrane is generated once. If one decides to change the position of the generated membrane, first the membrane must be deleted pressing the "Delete" button, reposition the box, and generate the membrane again.

• Translate/Rotate: the action generated by the movers "--", "-", "+" and "++".
• x / y / z: axis for translation/rotation.
• -- / ++ buttons: membrane temporary box movers to translate the box by -5 Å or +5 Å, or rotate -15° or +15° over the selected axis.
• - / + buttons: membrane temporary box movers to translate the box by -1 Å or +1 Å, or rotate -1° or +1° over the selected axis.
• Generate: Generate the membrane according to the location and dimension of the temporary box.
• Delete: Delete the previous generated membrane.
• Optimize Size: Change the center and dimensions (orientation is not affected) of the membrane to ensure that the existence of at least 15 Å between protein maximum and minimum coordinates and simulation cell limits in the membrane axis.

  Note: The periodic boundary conditions dimensions, in the membrane axis, are determined by the membrane dimensions.

One can apply structure modifications by listing the sequence of patches, following the specific command format, "PatchName ChainID1 ResidueNumber1" or in cases of 5 arguments patches "PatchName ChainID1 ResidueNumber1 ChainID2 ResidueNumber2". The list of modifications can be found in the CHARMM36 topology and stream files with the keyword "PRES".

• Save: Save all the operations performed and options to the QwikMD input file (*.qwikmd)
• Load: Load a previous generated QwikMD input file. If one ore more protocol steps had been already performed, one can use the dialog window to the steps to be loaded into VMD.
• Reset: Return QwikMD to the initial state and set all the options to the default value. If a simulation is being performed in "Live View" Mode, QwikMD will terminate the simulation during the reset process.
• Live View: Run the simulation in "Live View" Mode. Within "Live View" Mode, one can visualize the simulation while it is being calculated, useful for demonstration purpose and for quick system inspection. During the "Livew View" simulation, one can also perform live analysis, in which the properties, like Root Mean Square Deviation (RMSD) and energies components are calculated and displayed, concurrently with the simulation calculation.

  WARNING: This option must be selected before pressing the button "Prepare".

• Prepare: Prepare the system for simulation and generate the configuration files necessary to execute NAMD. The system preparation phase is composed by the following steps: structure manipulation operations selected by the user such as point mutations and protonation state assignment; membrane insertion; system solvation and salt addition to neutralize and achieve the desired concentration (if applicable). QwikMD keeps track of every options and operations performed by the user and stores the information in two log file: the QwikMD input file and "InputFileName".infoMD.
  • QwikMD input file (*.qwikmd) is a script compiling all the options selected and operation performed by the user and can be loaded back into QwikMD.
  • "InputFileName".infoMD is a human readable text file, where one can review all the steps taken regarding the system preparation, methods and the correspondent citation articles employed in the simulations and the analysis carried over the simulations.
• Start Simulation: Execute the protocol step listed in the button text. In the case of "Live View" mode simulations, one can visualize and perform live analysis, otherwise, NAMD will be executed in the background and QwikMD and VMD will be inaccessible ("froze") until the simulation is completed.

  Easy Run: On "Easy Run" tab, one can extend the MD or SMD simulation step (depending on the current selected protocol) by pressing this button again, where a new MD or SMD simulation is started from the last point of the previous simulation. The extended simulation are numbered sequentially and latter loaded into QwikMD in the same order.

  Advanced Run: On "Advanced Run" tab, one can extend the last simulation on the current protocol by adding an additional step to the protocol and press the this button to start the simulation from the last point of the previous simulation. The extended simulation are numbered sequentially and latter loaded into QwikMD in the same order.

  Run Simulations On Supercomputers: To perform the simulations prepared with QwikMD on a supercomputer, one must copy the "run" folder to the the supercomputer file system and run NAMD following the procedures for the specific computer.

• Pause: Pause a "Live View" simulation
• Detach: Stop a "Live View" simulation without update the coordinates. Use this button it if anything goes wrong.
• Finish: Stop a "Live View" simulation and update the coordinates.
• Progress bar: Display the current progress of a "Live View" simulation.

  Note: During a "Live View" simulation, QwikMD gui is updated on a fix interval of simulation steps. If the simulation finishes before the completion of the interval, QwikMD can not detect the increment to update the progress bar as well as the simulation termination. In this case one must press "Finish" to enforce the update of QwikMD. The message Info) IMD connection ended unexpectedly; connection terminated on the VMD terminal window indicates that the simulation stopped/finished.

• Don't load water/solvent ion molecules or hydrogen atoms: trajectory pre-load treatment to remove the water/solvent ion molecules or hydrogen atoms and therefore reduce the size of the trajectory files to be loaded into VMD. Depending on the size of the trajectory, this step may take a long time to perform, however is only performed once per combination of selected options. This pre-treatment creates a new trajectory file (*.dcd) in the "run" folder with a suffix "_" In the subsequent loading This options uses the CatDCD program only available the Unix (Linux & Mac) versions of VMD.
• Select Trajectories: select the trajectories to be loaded into VMD. Only the selected trajectories will be considered for analysis as well as the correspondent simulation log files, containing the values of the energy components (bonds, angles and etc.), SMD forces, temperature, volume and pressure.
• Loading Trajectory Frame Step (Stride): select every Stride frames from the beginning to the end of the trajectory. Default value is 1, meaning loaded all frames stored in the trajectory file.

• Region selection: the first atom selection regards the structure region where the RMSD will be calculated. One can use the drop-down menu to select the pre-defined selection OR type the atom selection in the text entry, using VMD atomselection syntax.
• Align Structure: align each frame with the first frame loaded into VMD. Like the "Region Selection", one can select the alignment target region using the drop-down menu OR typing the atom selection in the text entry, using VMD atomselection syntax.

More advanced options for RMSD analysis can be done with VMD plugins available in VMD Main menu item Extensions - Analysis. To read more about VMD and its plugins check the VMD plugins webpage.