Re: Colvars and distance restraint for umbrella sampling

From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Tue Oct 16 2018 - 19:41:21 CDT

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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