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lqz Offline OP
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Dear all:

I ran umbrella-sampling simulations using CHARMM implicit simulations and gbsw module on 37 windows with the protein aligned on different heights in z-direction relative to the lipid bilayer. After that, I plan to use WHAM program to combine the result and calculate PMF. I am wondering how to determine the spring constant in the metafile for running the wham command:

# /path/to/timeseries/file loc_win_min spring [temperature]

Thanks a lot.

lqz

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The spring constant for the (WHAM)analysis is the same as what you used in the simulations. Note that if you used the CHARMM command "CONS HARM FORCE k" for the US simulations, the standard form of the biasing potential is Ebias=k(x-xref)**2; note that there is no factor "0.5" in the energy expression.


Lennart Nilsson
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Thanks a lot for the information.
I used MMFP command to restrain the z-axis height. In the output file, I have the following content:

DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA MMFP: GEO MDIP SSBP SHEL DROFfa
DYNA PBEQ: PBnp PBelec GBEnr GSBP SMBP
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
---------- --------- --------- --------- --------- ---------
DYNA> 0 10300.00000 -2086.84104 1418.15899 -3505.00003 322.33517
DYNA PROP> 21.25801 -2070.70137 1450.16175 16.13967 1964.17523
DYNA INTERN> 548.84619 800.48610 115.11011 508.89445 50.92207
DYNA EXTERN> -267.88708 -4116.45492 0.00000 48.34767 0.00000
DYNA MMFP> 4.19108 0.00000 0.00000 0.00000 0.00000
DYNA PBEQ> 0.00000 0.00000 -1197.45570 0.00000 0.00000
DYNA PRESS> -1146.50897 -162.94119 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

Can I say MMFP equals to 4.19108 is the parameter for this step?

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Uh?

The MMFP energy at this time-step seems to be 4.12 kcal/mol, but I don't know how you want to use this information in your WHAM-analysis.
How about posting the relevant input?

Please do discuss with your supervisor!!


Lennart Nilsson
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The spring constant is the force you specified for the restraint, regardless of whether the command was CONS HARM, CONS HMCM, or the MMFP command GEO PLANAR.


Rick Venable
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lqz Offline OP
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Because of the internet problem, I did not post my previous message correctly. Sorry for the miscommunication.
Thank you for the information. My question was answered, and I know how to decide k now.

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Hi,

I am also doing a similar kind of simulation where I am restraining my molecules on a plane using CONS HMCM command and using SSBP with umbrella sampling.

So should my metadata be of this format?

# /path/to/timeseries/file loc_win_min spring [temperature]
................../fort3.dat 3.0 4.0

I used 2.0 kcal/mol/A2 as force constant for umbrella sampling in CHARMM. So I am doubling it to be used for WHAM analysis.

The CONS HARM FORCE 100.0 also is a type of restraint.
How should I add this to WHAM metadata to get unbiased results?


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