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

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Mon Feb 25 2008 - 13:48:55 CST

Hi!

This is how I would do it - it might be the simpler way.
 
As soon as you are able to constrain your desired
"coordinate/coordinates" (and this can be done very easily in tclforce
in namd) you are done. You will just have to output to a file (each for
your each window along the pre-defined path) the instantaneous values of
the "coordinate", constraining force constant and equilibrium value and
feed those to a WHAM program (that you can find easily on the web).

I am sure that there might other nicer ways . I would look in the free
energy calculation chapter of the NAMD manual.

George Giambasu
Phd Student, UMN

Xu, Jiancong wrote:
> 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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