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HOW TO RUN NAMD

HOW TO RUN NAMD. Protein structure File. Tutorial web page:. http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/. NAMD configuration parameters ; Timestep parameters

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HOW TO RUN NAMD

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  1. HOW TO RUN NAMD

  2. Protein structure File

  3. Tutorial web page: • http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/

  4. NAMD configuration parameters ; Timestep parameters • numsteps number of timesteps >Acceptable Values: positive integer Description: The number of simulation timesteps to be performed. An integer greater than 0 is acceptable. The total amount of simulation time is numsteps x timestep. • timestep <timestep size (fs) > Acceptable Values: non-negative decimal Default Value: 1.0 Description: The timestep size to use when integrating each step of the simulation. The value is specified in femtoseconds. • firsttimestep <starting timestep value >Acceptable Values: non-negative integer Default Value: 0 Description: The number of the first timestep. This value is typically used only when a simulation is a continuation of a previous simulation. In this case, rather than having the timestep restart at 0, a specific timestep number can be specified. • stepspercycle <timesteps per cycle> Acceptable Values: positive integer Default Value: 20 Description: Number of timesteps in each cycle. Each cycle represents the number of timesteps between atom reassignments. For more details on non-bonded force evaluation, see Section 5.1.

  5. Simulation space partitioning • cutoff local interaction distance common to both electrostatic and van der Waals calculations (Å) Acceptable Values: positive decimal Description: See Section 5.1 for more information. • switching use switching function Acceptable Values: on or off Default Value: off Description: If switching is specified to be off, then a truncated cutoff is performed. If switching is turned on, then smoothing functions are applied to both the electrostatics and van der Waals forces. For a complete description of the non-bonded force parameters see Section 5.1. If switching is set to on, then switchdist must also be defined. • switchdist distance at which to activate switching function for electrostatic and van der Waals calculations (Å) Acceptable Values: positive decimal cutoff Description: Distance at which the switching function should begin to take effect. This parameter only has meaning if switching is set to on. The value of switchdist must be less than or equal to the value of cutoff, since the switching function is only applied on the range from switchdist to cutoff. For a complete description of the non-bonded force parameters see Section 5.1.

  6. pairlistdist distance between pairs for inclusion in pair lists (Å) Acceptable Values: positive decimal cutoff Default Value: cutoff Description: A pair list is generated pairlistsPerCycle times each cycle, containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated. This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list. This parameter is equivalent to the X-PLOR parameter CUTNb. If no atom moves more than pairlistdistcutoff during one cycle, then there will be no jump in electrostatic or van der Waals energies when the next pair list is built. Since such a jump is unavoidable when truncation is used, this parameter may only be specified when switching is set to on. If this parameter is not specified and switching is set to on, the value of cutoff is used. A value of at least one greater than cutoff is recommended. • Etc....

  7. Simulatinf poly-alanine

  8. # This is a test namd configuration file timestep 1.0 numsteps 100000 structure alanin.psf parameters alanin.params coordinates alanin.pdb exclude scaled1-4 1-4scaling 0.4 outputname output margin 1.0 stepspercycle 20 temperature 300 langevin on langevinDamping 5 langevinHydrogen no langevinTemp 300 switching on switchdist 7.0 cutoff 8.0 pairlistdist 9.0 IMDon yes IMDport 2030 IMDfreq 1 IMDwait on

  9. Generating a Protein Structure File (PSF) • Of the four files (pdb, psf, topology and energy parameter files), an initial pdb file will typically be obtained through the Protein Data Bank, • and the parameter and topology files for a given class of molecule may be obtained via the Internet at http://www.pharmacy.umaryland.edu/faculty/amackere/force fields.htm. • The psf file must be created by the user from the initial pdb and topology files.

  10. REMARK FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PDB" REMARK PARAM11.PRO ( from PARAM6A ) REMARK =========== REMARK PROTEIN PARAMETERS: REMARK PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) REMARK TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) REMARK LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 REMARK CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. REMARK JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 REMARK DATE:16-Feb-89 11:21:32 created by user: nonella ATOM 1 CA ACE 1 -2.184 0.591 0.910 1.00 7.00 MAIN ATOM 2 C ACE 1 -0.665 0.627 0.966 1.00 0.00 MAIN ATOM 3 O ACE 1 -0.069 1.213 1.868 1.00 0.00 MAIN ATOM 4 N ALA 2 0.000 0.000 0.000 1.00 3.00 MAIN ATOM 5 H ALA 2 -0.490 -0.462 -0.712 1.00 0.00 MAIN ATOM 6 CA ALA 2 1.450 0.000 0.000 1.00 7.00 MAIN ATOM 7 CB ALA 2 1.969 -0.670 -1.262 1.00 0.00 MAIN ATOM 8 C ALA 2 2.010 1.413 0.000 1.00 0.00 MAIN ATOM 9 O ALA 2 2.911 1.748 0.767 1.00 1.00 MAIN ATOM 10 N ALA 3 1.488 2.280 -0.863 1.00 0.00 MAIN ATOM 11 H ALA 3 0.770 1.998 -1.467 1.00 4.00 MAIN ATOM 12 CA ALA 3 1.981 3.643 -0.909 1.00 7.00 MAIN ATOM 13 CB ALA 3 1.147 4.464 -1.880 1.00 0.00 MAIN ATOM 14 C ALA 3 1.865 4.326 0.444 1.00 0.00 MAIN ATOM 15 O ALA 3 2.801 4.963 0.924 1.00 0.00 MAIN ATOM 16 N ALA 4 0.710 4.211 1.093 1.00 9.00 MAIN ATOM 17 H ALA 4 -0.026 3.700 0.697 1.00 0.00 MAIN ATOM 18 CA ALA 4 0.541 4.841 2.388 1.00 7.00 MAIN ATOM 19 CB ALA 4 -0.809 4.462 2.976 1.00 8.00 MAIN ATOM 20 C ALA 4 1.591 4.371 3.381 1.00 0.00 MAIN

  11. remark - parameter file PARAM19 - • remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) • remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) • remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 • set echo=false end • !! - PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974) • !! - PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) • !! - NONBONDED TERMS JORGENSEN JACS 103:3976 W/ RC1-4 = 1.80 EC1-4 = 0.1 • !! The default h-bond exponents are now 6-repul 4-attr • !! ++++++++ ATOMTYPE OS (IN METHYL ESTER) ADDED FOR CHARMM COURSE /LN ++++ • !! Switched from Slater-Kirkwood to simple mixing rules - AB • !! Hbond parameters based on comparisons of dimer results with • !! ab initio calculations. - WER 12/19/84 • !! Grouping of atom types for VDW parameters - BRB 1/3/85 • bond C C 450.0 1.38! B. R. GELIN THESIS AMIDE AND DIPEPTIDES • bond C CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT • bond C CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED • bond C CH3E 405.0 1.52 • bond C CR1E 450.0 1.38 • bond C CT 405.0 1.53 • bond C N 471.0 1.33 • bond C NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE • bond C NH1 471.0 1.33 • bond C NH2 471.0 1.33 • bond C NP 471.0 1.33 • bond C NR 471.0 1.33 • bond C O 580.0 1.23 • bond C OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O • bond C OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) • bond C OS 292.0 1.43! FROM DEP NORMAL MODE FIT

  12. By using topology file and parameter files you will create alanine.psf file • http://www.ks.uiuc.edu/Training/Tutorials/ namd/namd-tutorial-win.pdf

  13. Exercise: repeat the steps in the manual (for ubiquitin) and perform the anlyses in a water box for a temperature between 250 K and 400 K for 2 ns (how many time steps with 2 fs timestep). ASLIHAN 250 AYTUĞ 275 BESRAY 300 GÜNEŞ 325 GÜZİN 350 EMRE 375 MURAT 400 NURCAN 250 ORHAN 275 OSMAN 300 ÖZGE 325 PINAR 350 SEMİH 375 SİNAN 400 ŞERİFE 450

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