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MDynSBAbstractThe Program MDynSB is designed to perform multiple tasks with protein structure:
How to run the programProgram 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):
File names could be set from the command line. MdynPar.inpThe $ 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.
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 #END
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 $LoopMD $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 #END
The loop.inp file has the structure: #BPTI # tarters # endRes for the Loop #line format = (a6,i4,i4) LOOP1 15 20 LOOP2 40 44 end
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 $MDSA #END #SAprotocol #nSAstep 6 ! number of T step #(i8,2x,i8) #2345678**12345678 #ntimeMX tempt T,K 500 10 !number of MD step at the Temperature 500 20 500 30 500 40 500 50 500 50 # end PerformanceCPU time is 9-10 min per each 1000 MD step (on athlon 1400 MHz) for protein of about 3000 atoms. Detailed descriptionFor the most detailed description of the program and its features the reader is referred to MDynSB Manual (MS Word .doc format). |
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