From: Rui Zhang (zhangrui1002_at_gmail.com)
Date: Tue Aug 07 2012 - 18:11:32 CDT
Hi Giacomo,
Thanks for fixing the code!
I have a question about the system forces output. I've run some steer MD
and got system forces on the reaction coordinates. I'm wondering if there's
a way to average and integrate those forces to recover the energy along the
reaction coordinates. The .traj output is copied below. Another question
is: can we use NAMD to read in a pre-calculated trajectory and calculate
the values of certain colvars? Thank you very much!
Best,
Rui
# step BaseDistance fs_BaseDistance
BHDistance fs_BHDistance TLDistance
fs_TLDistance
0 9.62747676503525e+00 0.00000000000000e+00
1.50126297850794e+01 0.00000000000000e+00 1.88680762897573e+01
0.00000000000000e+00
100 9.66876657393063e+00 -2.55060584730339e+01
1.49725563253941e+01 -1.69237620485508e+01 1.89725005214356e+01
-9.35492521567175e+00
200 9.70544967550636e+00 -1.85276943308032e+01
1.47747124226418e+01 1.41160046798081e+01 1.90807057671530e+01
2.82023033829673e+01
300 9.66192423080611e+00 -1.87705714340321e+01
1.48654309057713e+01 1.76387579131218e+01 1.90645186317176e+01
4.88415350117261e+01
400 9.58527332714355e+00 -9.07363469579865e+00
1.49140037594118e+01 -8.59231345668682e+00 1.89958040409527e+01
6.22762562339921e+01
500 9.58027289270208e+00 1.74962884799941e+01
1.47917404446112e+01 4.01007189039577e+01 1.89736009040358e+01
-5.88112555983224e+01
600 9.68592399876123e+00 -5.51021750743205e+01
1.46768306138277e+01 -2.70131662532274e+01 1.87211036305893e+01
6.99252751465140e+01
700 9.54758709556370e+00 1.05429401635401e+01
1.47731707230182e+01 1.79187578682112e+00 1.86432458113661e+01
7.11905631955904e+01
800 9.45654761690041e+00 -8.25593452085068e+00
1.49603801874835e+01 6.15731151321220e+01 1.87173145051163e+01
3.76516841390899e+01
900 9.35042984449095e+00 2.54119309650548e+00
1.52075033826027e+01 1.21605848886426e+01 1.85571900579306e+01
6.49501101456375e+01
1000 9.24608840602325e+00 1.03184746388288e+01
1.52707514111075e+01 -1.54913865731315e+01 1.85852234586205e+01
-3.01331515291548e+01
1100 9.29630151429482e+00 -5.12837023815550e+01
1.50852295900376e+01 1.39198087349484e+01 1.85876251012541e+01
-1.21200698685873e+02
1200 9.31194901020928e+00 4.47336106929457e+00
1.49442912583056e+01 -2.02148583230082e+01 1.85954808259544e+01
1.00895551335830e+02
1300 9.38236037189959e+00 -1.66270322283634e+01
1.49357493051093e+01 -2.57517786302922e+01 1.86236453918922e+01
-4.57355014097964e+01
1400 9.42696331662386e+00 -3.04206596217194e+01
1.48004816167103e+01 2.21891380113082e+01 1.85676965081666e+01
4.20240693181712e+01
On Mon, Aug 6, 2012 at 10:20 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> Hello Rui, I found the error: sorry about the inconvenience. In the last
> code change of the section that writes final output files some time ago,
> the coorFunc-related output was accidentally disabled.
>
> Can you recompile NAMD? If so, I could send you a patch that fixes this
> temporarily.
>
> On Thu, Aug 2, 2012 at 8:06 PM, Rui Zhang <zhangrui1002_at_gmail.com> wrote:
>
>> Hi,
>> I was trying to calculation the auto-correlation function for a colvar.
>> But the corrfunc.dat file was produced even though the calculation was
>> finished successfully. And the output showed:
>>
>> colvars: Initializing a new collective variable.
>> colvars: # name = Lysdist
>> colvars: Initializing a new "distance" component.
>> colvars: # componentCoeff = 1 [default]
>> colvars: # componentExp = 1 [default]
>> colvars: # period = 0 [default]
>> colvars: # wrapAround = 0 [default]
>> colvars: # forceNoPBC = off [default]
>> colvars: # oneSiteSystemForce = off [default]
>> colvars: Initializing atom group "group1".
>> colvars: Atom group "group1" defined, 1 initialized: total mass =
>> 15.9994.
>> colvars: Initializing atom group "group2".
>> colvars: Atom group "group2" defined, 1 initialized: total mass =
>> 14.007.
>> colvars: All components initialized.
>> colvars: # width = 1 [default]
>> colvars: # lowerBoundary = 0 [default]
>> colvars: # lowerWallConstant = 0 [default]
>> colvars: # upperBoundary = 0 [default]
>> colvars: # upperWallConstant = 0 [default]
>> colvars: # expandBoundaries = off [default]
>> colvars: # extendedLagrangian = off [default]
>> colvars: # outputValue = on [default]
>> colvars: # outputVelocity = off [default]
>> colvars: # outputSystemForce = off [default]
>> colvars: # outputAppliedForce = off [default]
>> colvars: # runAve = off [default]
>> colvars: # corrFunc = on
>> colvars: # corrFuncWithColvar = "Lysdist" [default]
>> colvars: Calculating auto-correlation function.
>> colvars: # corrFuncType = coordinate
>> colvars: # corrFuncOffset = 0 [default]
>> colvars: # corrFuncLength = 1000
>> colvars: # corrFuncStride = 1 [default]
>> colvars: # corrFuncNormalize = on [default]
>> colvars: # corrFuncOutputFile = "stats2.Lysdist.corrfunc.dat" [default]
>>
>> Could you help me check why there's no output for corrfunc? Thank you!
>>
>> Rui
>>
>
>
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