Re: Colvars and distance restraint for umbrella sampling

From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Wed Oct 17 2018 - 10:58:13 CDT

You are right. The force constant is very high. Showing 12500 in the log
file.

Regards,

On Wed, Oct 17, 2018 at 11:49 AM Gumbart, James C <
gumbart_at_physics.gatech.edu> wrote:

> I think the forceconstant you are using is way too high. I believe the
> scaling by the width goes in the other direction, i.e., you are using a
> force constant of 50,000 kcal/mol*A^2. Can you please check your logfile
> to confirm? It will say something like “Force constant for ___ rescaled
> to…”. I could be wrong.
>
> As for checking the overlap, you can plot the traj files directly and then
> make histograms from them (xmgrace, for example, can easily do this). The
> tutorial also gives ways to determine this, and other things to check, on
> pages 23-25.
>
> Best,
> JC
>
> On Oct 17, 2018, at 11:41 AM, Udaya Dahal <dahal.udaya_at_gmail.com> wrote:
>
> Hi JC,
>
> I didn’t run the tutorial itself but i am able to run the US now . The
> only difference I noticed is the force constant used in the tutorial is not
> able to constraint my peptide in the target center. I significantly
> increased the value which is now restraining the peptide around center of
> mass. Currently I have 20 windows of separation width of 1Angstrom and I am
> using 0.1 in the colvar width. How do we know if the neighboring windows
> overlap and how do we determine what force constant to use? Here is my
> recent colvar script
>
> colvarsTrajFrequency 20
> colvarsRestartFrequency 5000
>
>
> colvar {
> name Translocation
>
> width 0.1
>
> lowerboundary 40.0
> upperboundary 100.0
>
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
> distance {
> group1 { atomnumbers {7301 7302 7303 7304 7305 7306 7307 7308 7309
> 7310 7311 7312 7313 7314 7315 7316 7317 7318 7319 7320 7321 7322 7323 7324
> 7325 7326 7327 7328 7329 7330 7331 7332 7333 7334 7335 7336 7337 7338 7339
> 7340 7341 7342 7343 7344 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354
> 7355 7356 7357 7358 7359 7360 7361 7362 7363 7364 7365 7366 7367 7368 7369
> 7370 7371 7372 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 7384
> 7385 7386 7387 7388 7389 7390 7391 7392 7393 7394 7395 7396 7397 7398 7401
> } }
> group2 { atomnumbers { 1910 }}
> }
> }
>
> harmonic {
> colvars Translocation
> centers 11.5
> forceConstant 500;# 500 * 0.1^2 = 5kcal/mol
> Regards,
>
> On Oct 17, 2018, at 11:27 AM, Gumbart, James C <gumbart_at_physics.gatech.edu>
> wrote:
>
> If you find something taken directly from that tutorial no longer works,
> please let me know.
>
> You don’t say what error you got, so it’s difficult to make suggestions
> (other than what Giacomo noticed). Also, regarding center of mass, I think
> all multi-atom colvar components use the center of mass (or geometry?) by
> design.
>
> Best,
> JC
>
> On Oct 16, 2018, at 8:41 PM, Udaya Dahal <dahal.udaya_at_gmail.com> wrote:
>
> Thank you Giacomo for the quick response. I am currently using NAMD 2.12
> and the tutorial i was following is
> https://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf
> .
>
> Regards,
>
> On Tue, Oct 16, 2018 at 8:31 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Please check the manual for the harmonic restraint:
>>
>> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic
>> it is "centers" (plural), not "center".
>>
>> In general, you should reference which version of NAMD you are using
>> (different versions include different version of the Colvars module, of
>> course), and the following if needed:
>>
>> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_config_changes
>>
>> Lastly, please mention also what tutorial you are referring to (with
>> link), because not all tutorials are up to date.
>>
>> Giacomo
>>
>> On Tue, Oct 16, 2018 at 8:09 PM Udaya Dahal <dahal.udaya_at_gmail.com>
>> wrote:
>>
>>> Hi Everyone,
>>>
>>> I am trying to calculate PMF for a peptide chain bound to surface. I
>>> have a fixed surface and the reaction coordinate is along z-direction. For
>>> umbrella sampling, I need to restrain my peptide's center of mass at
>>> specific point along z direction. For this I used one (fixed atom) from
>>> surface as a reference atom and peptides atoms as group of atoms for
>>> "distanceZ" module in namd, The script is as follows similar to that in the
>>> tutorial. The following description doesn't seem to define center of mass
>>> of the atoms for the "main" which led to crashing the simulation( my
>>> assumption). The "distance" module seems defines two center of mass groups
>>> but there is no option for restraining along particular axis. I would
>>> appreciate if there is any suggestion on how to proceed from here.
>>> colvar {
>>> name Translocation
>>> width 0.1
>>> lowerboundary 40.0
>>> upperboundary 100.0
>>> lowerwallconstant 100.0
>>> upperwallconstant 100.0
>>> distanceZ {
>>> main {
>>> atomnumbers { 7301 7302 7303 7304 7305 7306 7307 7308 7309 7310
>>> 7311 7312 7313 7314 7315 7316 7317 7318 7319 7320 7321 7322 7323 7324 7325
>>> 7326 7327 7328 7329 7330 7331 7332 7333 7334 7335 7336 7337 7338 7339 7340
>>> 7341 7342 7343 7344 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354 7355
>>> 7356 7357 7358 7359 7360 7361 7362 7363 7364 7365 7366 7367 7368 7369 7370
>>> 7371 7372 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 7384 7385
>>> 7386 7387 7388 7389 7390 7391 7392 7393 7394 7395 7396 7397 7398 7399
>>> }
>>> }
>>> ref {
>>> atomnumbers { 1910
>>> }
>>> }
>>> axis ( 0.0, 0.0, 1.0 )
>>> }
>>> }
>>>
>>> harmonic {
>>> name Z
>>> colvars Translocation
>>> CENTER 11.5
>>> forceConstant 0.025
>>> }
>>>
>>> Regards,
>>> Udaya
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
>
>

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