Re: nvt input file

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Fri Jul 17 2015 - 08:44:24 CDT

Ursula,

If you need 'permanent' restrains (i.e. not adaptive ones), you should
specify this in separate pdb file using B-column for atoms on which
restraints should be applied
Example:

ATOM 7 H3 GLY A 24 24.292 15.846 14.617 1.00 0.00
A1 H
ATOM 8 HA1 GLY A 24 26.568 17.825 14.994 1.00 0.00
A1 H
ATOM 9 HA2 GLY A 24 26.802 16.041 15.084 1.00 0.00
A1 H
ATOM 10 N SER A 25 26.103 17.910 17.512 1.00 *0.10* A1 N
ATOM 11 CA SER A 25 25.677 17.988 18.936 1.00 *0.10* A1 C
ATOM 12 C SER A 25 24.545 19.045 18.970 1.00 *0.10* A1 C
ATOM 13 O SER A 25 24.156 19.674 17.998 1.00 *0.10* A1 O
ATOM 14 CB SER A 25 26.925 18.317 19.801 1.00 0.00
A1 C
ATOM 15 OG SER A 25 27.368 19.574 19.322 1.00 0.00
A1 O
ATOM 16 H SER A 25 26.799 18.564 17.193 1.00 *0.10* A1 H
ATOM 17 HA SER A 25 25.339 17.024 19.250 1.00 0.00
A1 H
ATOM 18 HB1 SER A 25 27.539 17.480 19.486 1.00 0.00
A1 H
ATOM 19 HB2 SER A 25 26.624 18.367 20.856 1.00 0.00
A1 H

So if value is 20 kcal, you should add value of 20 in this column for
chosen atoms. Please be aware that this is very large value, in this way
you most probably will fix atoms in particular positions. In addition in
NAMD configuration file you should add following lines:

# Harmonic constraints
constraints on
consexp 2
conskcol B
constraintScaling 1.000000
conskfile name-of-pdb-files-with-restraints.pdb
consref can be same file as above, or initial pdb file.pdb

You could find more details in NAMD tutorials and NAMD user guide

Branko

On 7/17/2015 3:25 PM, Urszula Uciechowska wrote:
> Dear NAMD users,
>
> Below is the input file that I prepared for my nvt run for protein-DNA
> complex. Please have a look at it as I am new to namd and not sure if it
> is correct.
> I would like to also set up harmonic restraints 20kcal to the backbone
> atoms how could I add it to this input file? In amber I can simple add
> the line restraintmask=':1-285_at_CA,N,C,O',restraint_wt=20. How to do it in
> namd.
>
>
> ## USER VARIABLES
> set outPrefix output/model4-nvt
> set inPrefix output/model4-npt.restart
> set temperature 300
>
>
> ##Output
> outputName $nvt; # this tells namd where to write output files
>
> ##Number of steps between output writes
> dcdfreq 1000; # simulation trajectory
> restartfreq 500; # 500 steps = every 1ps
> xstFreq 500; # XSTFreq: control how often the extended
> system configuration will be appended to the XST file
> outputEnergies 125; # 125 steps = every 0.25ps
> outputPressure 125; # info about the pressure (printed in log file)
> outputTiminig 500; # the number of timsteps between each
> timinig output shows the time per step and time to completion
>
> ##Input
> structure ssb.psf; # initial structure file
> coordinates ssb.pdb; # initial coordinate file
>
> cellBasisVector1 86.313 0 0
> cellBasisVector2 0 88.430 0
> cellBasisVector3 0 0 83.732
>
> firstTimeStep 0; # only affects dynamics for SMD simulations
>
> ##Restart files
> binCoordinates $min.coor
> binVelocities $min.vel
>
> COMmotion yes; # always (default is no and removes the
> center
> # of mass velocity whenever you restart a
> simulation
>
>
> #Constant pressure simulation
> langevinPiston on; # turn this off for constant volume sim
> langevinPistonTarget 1.01325; # in bar -> 1 atm
> langevinPistonPeriod 50
> langevinPistonDecay 25
> langevinPistonTemp $temperature
>
> #Constant Temperature Control
> langevin on; # langevin dynamics
> langevinDamping 3.0; # dumping coefficient
> langevinTemp $temperature
> langevinHydrogen no; # do not couple the bath to hydrogens
>
> ## additional
> useGroupPressure yes; # yes = don't
> # needed for rigidBonds (see rigidBonds below)
> useFlexibleCell no; # allow x,y,z dimensions to fluctuate
> independently?
> # useConstantArea no; # if so, fix area of xy-plane?
> # useConstantRatio no; # OR if so, fix aspect ratio of xy-plane?
>
> ## affects output coordinates only, not dynamics
> # wrapAll on; # since we use periodic boundary conditions
> we keep everything in one unit cell
> wrapWater on
>
>
> ##FORCES##
>
> ## multiple timestepping: calculate some forces less frequently
> timestep 2; # use 2fs timestep (for bonded interactions)
> # all the other "frequencies" (really periods)
> # are in terms of this
>
> nonBondedFreq 1; # vdW and short range electrostatics every 2fs
> fullElectFrequency 1; # long range electrostatics every 6fs
> stepsPerCycle 20; # re-evaluate parilistdist after this many steps
> pairlistsPerCycle 2; # default value
>
> ## bonded interactions
> rigidBonds all; # freezes bond length between hydrogen and other
> atoms
> # which is the fastest vibrational mode in an MD
> sim
> timestep 2.0; # holding this rigid allows 2fs timestep
>
>
> exclude scaled1-4; # scale vdW interaction for bonded
> atoms
> 1-4scaling 1.0; # use 0.833333333 for Amber parameters
>
> ## short-range interactions
> switching on; # smoothly turn off vdW interactions at cutoff
> vdwForceSwitching yes; # new option for force-based switching of vdw
> switchDist 10; # start turning vdW interaction off (Å)
> cutoff 12; # only calc short range interactions inside this (Å)
> pairlistdist 10; # every stepPerCycle, each atom updates its list
> # of atoms it may be interacting with during
> # the following cycle, using this distance (Å)
>
> ## long-range interactions (particle-mesh ewald for long-range
> electrostatics)
> PmeGridSpacing 2.0; # this is larger than the usual number
> PME yes
> PMEGridSizeX 120
> PMEGridSizeY 120
> PMEGridSizeZ 120
>
> ## Force-Field Parameters
> paraTypeCharmm on; # we always use CHARMM
> formatted parameters (even when using Amber)
> parameters par_all36_na.prm; # parameter file specifies
> how atoms should interact
> parameters par_all36_prot.prm; # parameter file specifies
> how atoms should interact
> parameters par_water_ions_na.prm; # parameter file specifies
> how atoms should interact
>
> ###Run
> minimize 2500
> run 2500
>
> Thank you for any suggestions
>
> best regards
> Urszula Uciechowska
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>

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