From: Bryan Roessler (roessler_at_uab.edu)
Date: Mon Dec 14 2015 - 12:41:08 CST
Giacomo,
It is the same value, so it appears that the W-<variable name> is indeed
the accumulating work.
The reason I am confused is that the accumulated work seems to increase
harmonically, whereas in other published experiments the accumulating work
is dependent on the reaction coordinate (transition tube). As the protein
progresses down its favorable transition state, the accumulating work
should slow, and as it enters unfavorable metastable states, it should grow
faster (to pull the protein out of those states towards the targeted
structure). I'm seeing a perfectly harmonic curve. Could this be caused by
a force constant that is too high?
I'm working on a fairly large membrane transporter and am using a K of 200
kcal/mol as is recommended by the NAMD manual as a good starting point for
C-alpha TMD (except that I am using the colvar module and not the built-in
method).
Thanks,
Bryan
*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb <http://uab.edu/cmdb>*
Knowledge that will change your world
On Mon, Dec 14, 2015 at 10:55 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hello Bryan, the output is in the column labeled as "W_<variable name>".
>
> Does the last number in that column correspond to what you have in the
> state file?
>
> Giacomo
>
> On Sun, Dec 13, 2015 at 8:36 PM, Bryan Roessler <roessler_at_uab.edu> wrote:
>
>> Hello,
>>
>> I am performing an RMSD TMD using the colvar module. I have enabled
>> outputaccumulatedwork, defined colvarsTrajFrequency in my colvars.conf
>> file, and set a targetCenters as 0.
>>
>> #colvars.conf
>> colvarsTrajFrequency 100
>>
>> colvar {
>> name RMSD
>> outputAppliedForce on # keep track of bias force on this variable
>> rmsd {
>> atoms {
>> atomsfile target.pdb # Select biased atoms from this file
>> atomsCol O # based on occupancy (all nonzero values)
>> }
>> refPositionsFile target.pdb # ref. positions are selected based on
>> atom number
>> }
>> }
>>
>> harmonic { # Define a moving harmonic restraint
>> colvars RMSD
>> centers 8.108955 # go from x Angstrom RMSD...
>> targetCenters 0.0 # ... to 0 Angstrom
>> targetNumSteps 5000000 # in 5 million MD steps
>> forceConstant 200. # in kcal/mol/A^2
>> outputAccumulatedWork yes # keep track of how much energy will be
>> added
>> }
>>
>> In my colvars.traj file, I get the following result:
>>
>> # step RMSD fa_RMSD
>> W_harmonic1
>> 0 8.10893758151549e+00 3.48369690286177e-03
>> -5.64982828378909e-09
>> 100 8.11052619012773e+00 -3.46673845550072e-01
>> 5.65938731303684e-05
>> 200 8.11502663013762e+00 -1.27919766752989e+00
>> 1.31113744891078e-04
>> 300 8.11885738603493e+00 -2.07778466699651e+00
>> 3.83688077215023e-04
>> 400 8.12532180221536e+00 -3.40310372308537e+00
>> 8.18258935522487e-04
>> 500 8.12519728600043e+00 -3.41063630010119e+00
>> 1.44251410460275e-03
>> 600 8.10888978266427e+00 -1.81571452874252e-01
>> 1.78822263431076e-03
>> 700 8.10725589897312e+00 1.12769465353679e-01
>> 1.71416299364519e-03
>> 800 8.11735001417091e+00 -1.93848939420818e+00
>> 2.02673879603268e-03
>> 900 8.11555019832383e+00 -1.61096204479421e+00
>> 2.34953782273829e-03
>> 1000 8.11527862312204e+00 -1.58908282444123e+00
>> 2.65996804746196e-03
>> 1100 8.11598268331998e+00 -1.76233068403207e+00
>> 2.98824694512575e-03
>> 1200 8.11313380101662e+00 -1.22499004336234e+00
>> 3.29052949104976e-03
>> 1300 8.10521083280471e+00 3.27167779015269e-01
>> 3.28998207179514e-03
>> 1400 8.12048965688006e+00 -2.76103285605771e+00
>> 3.37644752668391e-03
>> 1500 8.11309309302196e+00 -1.31415590443957e+00
>> 3.70217004390935e-03
>> 1600 8.11441076220149e+00 -1.61012556035054e+00
>> 3.90344676028449e-03
>> 1700 8.11531243386224e+00 -1.82289571250216e+00
>> 4.13469721710158e-03
>> 1800 8.10407381960276e+00 3.92391319390129e-01
>> 4.30633172564267e-03
>> 1900 8.10543201783556e+00 8.83158528271366e-02
>> 4.25614003062294e-03
>> etc.
>>
>> and in traj.state:
>>
>> configuration {
>> step 5000000
>> dt 2.000000e+00
>> }
>>
>> colvar {
>> name RMSD
>> x 2.25972252769051e+00
>> }
>>
>> restraint {
>> configuration {
>> name harmonic1
>> centers -5.85060571139554e-10
>> centers_raw -5.85060571139554e-10
>> accumulatedWork 1.21825523336397e+03
>> }
>> }
>>
>>
>> So obviously the accumulated work is being calculated, but only output
>> when the .state file is written (final step), unless I'm missing it
>> elsewhere.
>>
>> Thanks,
>> Bryan
>>
>> *Bryan Roessler | Graduate Research Assistant*
>> UAB | The University of Alabama at Birmingham
>> *uab.edu/cmdb <http://uab.edu/cmdb>*
>> Knowledge that will change your world
>>
>>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> http://goo.gl/Q3TBQU
> http://giacomofiorin.github.io/
> https://icms.cst.temple.edu/members.html
>
>
>
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