Transcript Slide 1

HOW TO RUN NAMD
Protein structure File
Tutorial web page:
• http://www.ks.uiuc.edu/Research/namd/2.6
b1/ug/
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 nonbonded force evaluation, see Section 5.1.
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 nonbonded 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.
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....
Simulatinf poly-alanine
# This is a test namd configuration file
timestep
numsteps
structure
parameters
coordinates
exclude
1-4scaling
outputname
margin
stepspercycle
temperature
1.0
100000
alanin.psf
alanin.params
alanin.pdb
scaled1-4
0.4
output
1.0
20
300
langevin
on
langevinDamping 5
langevinHydrogen
langevinTemp
300
switching
switchdist
cutoff
pairlistdist
on
7.0
8.0
9.0
IMDon
IMDport
IMDfreq
IMDwait
yes
2030
1
on
no
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/fo
rce fields.htm.
• The psf file must be created by the user from the initial
pdb and topology files.
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PDB"
PARAM11.PRO ( from PARAM6A )
===========
PROTEIN PARAMETERS:
PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4
CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.
JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
DATE:16-Feb-89 11:21:32
created by user: nonella
1 CA ACE
1
-2.184
0.591
0.910 1.00 7.00
MAIN
2 C
ACE
1
-0.665
0.627
0.966 1.00 0.00
MAIN
3 O
ACE
1
-0.069
1.213
1.868 1.00 0.00
MAIN
4 N
ALA
2
0.000
0.000
0.000 1.00 3.00
MAIN
5 H
ALA
2
-0.490 -0.462 -0.712 1.00 0.00
MAIN
6 CA ALA
2
1.450
0.000
0.000 1.00 7.00
MAIN
7 CB ALA
2
1.969 -0.670 -1.262 1.00 0.00
MAIN
8 C
ALA
2
2.010
1.413
0.000 1.00 0.00
MAIN
9 O
ALA
2
2.911
1.748
0.767 1.00 1.00
MAIN
10 N
ALA
3
1.488
2.280 -0.863 1.00 0.00
MAIN
11 H
ALA
3
0.770
1.998 -1.467 1.00 4.00
MAIN
12 CA ALA
3
1.981
3.643 -0.909 1.00 7.00
MAIN
13 CB ALA
3
1.147
4.464 -1.880 1.00 0.00
MAIN
14 C
ALA
3
1.865
4.326
0.444 1.00 0.00
MAIN
15 O
ALA
3
2.801
4.963
0.924 1.00 0.00
MAIN
16 N
ALA
4
0.710
4.211
1.093 1.00 9.00
MAIN
17 H
ALA
4
-0.026
3.700
0.697 1.00 0.00
MAIN
18 CA ALA
4
0.541
4.841
2.388 1.00 7.00
MAIN
19 CB ALA
4
-0.809
4.462
2.976 1.00 8.00
MAIN
20 C
ALA
4
1.591
4.371
3.381 1.00 0.00
MAIN
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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
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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
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bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
bond C
C
450.0 1.38! B. R. GELIN THESIS AMIDE AND DIPEPTIDES
CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT
CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED
CH3E 405.0 1.52
CR1E 450.0 1.38
CT 405.0 1.53
N
471.0 1.33
NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE
NH1 471.0 1.33
NH2 471.0 1.33
NP 471.0 1.33
NR 471.0 1.33
O
580.0 1.23
OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O
OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
OS 292.0 1.43! FROM DEP NORMAL MODE FIT
• 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
•
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
AYTUĞ
BESRAY
GÜNEŞ
GÜZİN
EMRE
MURAT
NURCAN
ORHAN
OSMAN
ÖZGE
PINAR
SEMİH
SİNAN
ŞERİFE
250
275
300
325
350
375
400
250
275
300
325
350
375
400
450