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The Program MDynSB is designed to perform multiple tasks with protein structure:

  1. Optimization of a protein structure via MD simulation in an implicit water solvent.
  2. Optimization and folding of a protein via (the user defined) simulated annealing protocol in an implicit water solvent.
  3. Optimization of a predefined protein loops while non-loop parts of the protein molecule is kept fixed in the course of the loop optimization.

How to run the program

Program can be executed via the command with argument line

$> MdynSBex  -i  commandFile  -c myPDBfile -o myOUTfile -lp myLoopFile -sa mySAprotocFile

If the argument line does not define some argument file then the default fileName in the current dir will be used by program. Therefore, the user needs to prepare in the CURRENT dir the default name following input files for the MDynSB program (some of them might be omitted):

  • MDynPar.inp - the command file
  • molec.pdb - regular pdb file of the protein
  • loop.inp - defines start/end residue for Loops to be optimized
  • SAprotocol.inp - defines SimAnnealing Protocol

File names could be set from the command line.


The $ sign (in the first position of a line) defines a KEYWORD.

The # sign defines a comment.

Some keywords should be followed by a numerical or alphabetical value. The following table gives you the list of all keywords allowed. Default values presented in the table are used if the corresponding keyword is not specified.

The List of KEYWORDs
KeywordA short description
$LoopMDMD for defined LOOPs Note! line starting as # = comment
$fullProtMDMD for full protein
$SolvGSSolvation ON
$initMDTemp=10.0initial T
$bathMDTemp=50.0termalBath T
$runMDnstep=1000max N MD steps
$updateR1PL=10frequency to Update PAirList
$rcutV=8.0radius for VDW pairList
$rcutC=14.0radius for Coulombic pairList
$mdTimeStep=0.0010MD time step in ps
$NTV=1ensemble type NTV=1 or NTV=0,
$nwtra=200frequency to write SNAPshotsb for MD trajectory
$molecFile=./molec.pdbINput pdb proteinFile
$loopFile=./loop.inpLOOP start/end RES Numb
$fileSAProt=./SAprotocol.inpfile with SA protocol
$xyzMdTra=./xyzMd.traxyz trajectory
$engMdTra=./engMd.traenergy trajectory
$pdbMdTra=./molMdRes.pdbpdb trajectory
$pdbMdFin=./molMdFin.pdbpdb Final
$MDSA=NOMD with SIMulatedAnnealing protocol if not NO

Here is an examples of MdynPar.inp file.

To do initial Mdyn slow heat for full protein:

# example-1- do slow heat and make 3000 md time steps
# (3 ps - the total simulation time)
$fullProtMD               ! MD for full protein
$SolvGS                   ! Solvation ON
$initMDTemp=10.0          ! initial T 
$bathMDTemp=50.0          ! termalBath T   
$runMDnstep=3000          ! max N MD steps
$nwtra=200                ! frequency to write SNAPshotsb for MD trajectory

Program will write files in the current directory:

$xyzMdTra=./xyzMd.tra      !default - xyz trajectory
$engMdTra=./engMd.tra      !default   energy trajectory
$pdbMdTra=./molMdRes.pdb   !default   pdb trajectory
$pdbMdFin=./molMdFin.pdb   !default   pdb Final

Example 2 of MdynPar.inp

#  md for the defined loops
$SolvGS                    !Solvation ON
$initMDTemp=10.0           !initial T 
$bathMDTemp=50.0           !termalBath T   
$runMDnstep=3000           !max N MD steps
$nwtra=200                 !frequency to write SNAPshotsb for MD trajectory

The loop.inp file has the structure:

#  tarters 
#           endRes for the Loop
#line format = (a6,i4,i4)
LOOP1   15  20
LOOP2   40  44

Example 3 of MdynPar.inp

# Mdyn of full protein with Simulated Annealing protocol
# example-3- do slow heat, make 3000 md time steps
# (3 ps - the total simulation time),
# make SimulatedAnnealin Mdynamics
$fullProtMD                !MD for full protein
$SolvGS                    !Solvation ON
$initMDTemp=10.0           !initial T 
$bathMDTemp=50.0           !termalBath T   
$runMDnstep=3000           !max N MD steps
$nwtra=200                 !frequency to write SNAPshotsb for MD trajectory

Example of SAprotocol.inp:

6                          ! number of  T step
#ntimeMX  tempt T,K
500        10              !number of MD step at the Temperature
500        20
500        30
500        40
500        50
500        50


CPU time is 9-10 min per each 1000 MD step (on athlon 1400 MHz) for protein of about 3000 atoms.

Detailed description

For the most detailed description of the program and its features the reader is referred to MDynSB Manual (MS Word .doc format).