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HOW TO RUN NAMD. Protein structure File.

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Presentation on theme: "HOW TO RUN NAMD. Protein structure File."— Presentation transcript:

1 HOW TO RUN NAMD

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4 Protein structure File

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8 Tutorial web page: 6b1/ug/

9 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 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 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 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

10 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.5.1  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.5.1  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

11  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....

12 Simulatinf poly-alanine

13 # This is a test namd configuration file timestep1.0 numsteps structurealanin.psf parametersalanin.params coordinatesalanin.pdb excludescaled scaling0.4 outputname output margin1.0 stepspercycle 20 temperature300 langevinon langevinDamping 5 langevinHydrogenno langevinTemp300 switching on switchdist7.0 cutoff8.0 pairlistdist 9.0 IMDonyes IMDport2030 IMDfreq1 IMDwaiton

14 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 rce fields.htm. rce fields.htm The psf file must be created by the user from the initial pdb and topology files.

15 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: WITH 1-4 RC=1.80/0.1 REMARK DATE:16-Feb-89 11:21:32 created by user: nonella ATOM 1 CA ACE MAIN ATOM 2 C ACE MAIN ATOM 3 O ACE MAIN ATOM 4 N ALA MAIN ATOM 5 H ALA MAIN ATOM 6 CA ALA MAIN ATOM 7 CB ALA MAIN ATOM 8 C ALA MAIN ATOM 9 O ALA MAIN ATOM 10 N ALA MAIN ATOM 11 H ALA MAIN ATOM 12 CA ALA MAIN ATOM 13 CB ALA MAIN ATOM 14 C ALA MAIN ATOM 15 O ALA MAIN ATOM 16 N ALA MAIN ATOM 17 H ALA MAIN ATOM 18 CA ALA MAIN ATOM 19 CB ALA MAIN ATOM 20 C ALA MAIN

16 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: 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 ! B. R. GELIN THESIS AMIDE AND DIPEPTIDES bond C CH1E ! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT bond C CH2E ! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED bond C CH3E bond C CR1E bond C CT bond C N bond C NC ! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE bond C NH bond C NH bond C NP bond C NR bond C O bond C OC ! FORCE DECREASE AND LENGTH INCREASE FROM C O bond C OH ! FROM PARMFIX9 (NO VALUE IN GELIN THESIS) bond C OS ! FROM DEP NORMAL MODE FIT

17 By using topology file and parameter files you will create alanine.psf file namd/namd-tutorial-win.pdf

18 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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