RE: Re: umbrella sampling of decalanine using the ABF module

From: Xu, Jiancong (xuj1_at_ornl.gov)
Date: Mon Feb 25 2008 - 12:37:02 CST

A follow-up to this question, is there a way to do umbrella sampling calculations with NAMD? does NAMD offer such an option?

Thanks.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Jerome Henin
Sent: Mon 2/25/2008 11:44 AM
To: Philip Fowler
Cc: namd-l_at_ks.uiuc.edu
Subject: namd-l: Re: umbrella sampling of decalanine using the ABF module
 
Hi Phil,
usMode is but another abf-specific keyword, it's really a sub-command
of the abf keyword, like "coordinate" etc.
Jerome

On Mon, Feb 25, 2008 at 7:21 AM, Philip Fowler
<philip.fowler_at_bioch.ox.ac.uk> wrote:
> Hi,
>
> I am trying to reproduce the PMFs for the extension of decalanine from
> the NAMD/ABF paper [1]. I have successfully done this using adaptive
> biased forcing but now I want to try and use umbrella sampling.
>
> My problem is that NAMD does not appear to recognise the keyword
> "usMode" to force the ABF module to function in an umbrella sampling
> way. Even setting "usMode" to "no" results in NAMD dieing.
>
> I've tried moving the keyword around in the input file but NAMD always
> complains wherever it is. I am using NAMD2.6 and an example of my
> input file is appended. Any help would be gratefully appreciated.
>
> --Phil
>
> [1] J. Hénin and C. Chipot. Overcoming free energy barriers using
> unconstrained molecular dynamics simulations. J. Chem. Phys., 121(7):
> 2904-3004, 2004.
>
>
>
> #-----------------------------------------------------------------------------
> # BASIC parameters
> #-----------------------------------------------------------------------------
>
> temperature 301 # The initial temperature in K
> timestep 0.5 # Timestep in femtoseconds
> seed 19898473 # Allows repeatability of
> simulations.
> numsteps 4000000
>
> #-----------------------------------------------------------------------------
> # OUTPUT files.
> #-----------------------------------------------------------------------------
> outputname da-us-1.out
> restartname da-us-1.out.res
> velDCDfile da-us-1.out.vel.dcd
> DCDfile da-us-1.out.dcd
> XSTfile da-us-1.out.xst
>
> #-----------------------------------------------------------------------------
> # SETUP info
> #-----------------------------------------------------------------------------
>
> structure da.psf
> coordinates da.pdb
>
>
> paraTypeCharmm on
> parameters par_all27_prot_na.inp
>
> #-----------------------------------------------------------------------------
> # OUTPUT PARAMETERS
> #-----------------------------------------------------------------------------
>
> outputTiming 5000 # How often CPU times output
> outputEnergies 1000 # How often Energies are written
> to STDOUT
>
> binaryoutput yes # Use binary output files yes/no
> binaryrestart yes
> restartFreq 50000
> restartsave no
>
> DCDfreq 10000 # Interval between DCD trajector
>
> DCDUnitcell yes
> velDCDfreq 50000
>
> #-----------------------------------------------------------------------------
> # NON-BONDED PARAMETERS
> #-----------------------------------------------------------------------------
>
> dielectric 1 # Dielectric constant
>
> switching on # Smooth the transition
> switchdist 10 # Distance at which smoothing
> starts
> cutoff 12 # Distance at which all non-
> bonded interactions are zero
> pairlistdist 13.5 # Distance within which all
> atoms are considered for non-bonded
> # interactions. Must be greater than CUTOFF.
>
> stepspercycle 20
>
> PME off # Implement the Particle-Mesh-Ewald
> # electrostatics algorithm. Must be
> # used with periodic b.c.
> exclude scaled1-4 # Which bonded interactions
> to exclude from the non-bonded calculations
> 1-4scaling 1.0
>
>
> #-----------------------------------------------------------------------------
> # TEMPERATURE CONTROL
> #-----------------------------------------------------------------------------
>
> langevin on # use Langevin dynamics
> langevinTemp 300.0
> langevinDamping 1.0 # coupling coefficients to be
> applied to all atoms
> langevinHydrogen no # apply to hydrogens
>
>
> #-----------------------------------------------------------------------------
> # ADAPTIVE BIASED FORCE PARAMETERS
> #-----------------------------------------------------------------------------
>
> source /Users/fowler/packages/namd-2.6/lib/abf/abf.tcl
> abf coordinate distance
> usMode no
> abf abf1 3
> abf abf2 98
> abf dxi 0.1
> abf xiMin 12.0
> abf xiMax 32.0
> abf outFile da-1.abf.dat
> abf fullSamples 500
> abf inFiles {}
> abf distFile da-1.abf.dist
> abf dSmooth 0.0
>
> abf restraintList {
> dist1 {dist {BH 1 N} {BH 10 NT} 1.0 16.1}
> }
>
>
>
>

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