Re: Re: Multiple Colvars

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jul 25 2018 - 18:03:21 CDT

Hi Josh, thanks for pointing it out. Usually, unmatched braces are
detected during parsing. However, for those cases where the current logic
breaks, I just pushed to the Colvars repository an update (which you got
notified about) that checks for braces before anything else.

Giacomo

On Wed, Jul 25, 2018 at 11:28 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I was able to get a distanceZ + one dihedral colvar to work (so, 2D
> colvar), it appears that the atoms moving too fast was due to not selecting
> the atomnumbers in the correct order and/or incorrectly selecting one of
> the atom serial numbers.
>
>
> The memory error appears to be what Joshua suggested, not closing of one
> of the brackets and getting, essentially, an infinite loop using up all of
> the memory.
>
>
> Now, Giacomo or Joshua, since this is now a 2D (eventually going to 5D or
> more) PMF in that window, I cannot merge it with the other 1D windows,
> correct? Do I, therefore, need to add these dihedral colvars to all of my
> windows to make them the same dimension in order to merge them into one
> PMF? Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> *Sent:* Tuesday, July 24, 2018 3:59:23 PM
> *To:* McGuire, Kelly; namd-l_at_ks.uiuc.edu
> *Subject:* RE: Multiple Colvars
>
> I've had several hundred colvars in a configuration before, so in
> principle what you are doing ought to work, with the caveat that your
> colvar file needs to be parseable. I vaguely recall seeing this once when I
> didn't close a component definition, and the parser ran itself out of
> memory trying to find the end of the configuration file.
>
> -Josh
>
>
> On 2018-07-24 14:43:55-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> I'm still learning how to use colvars. As stated in other posts, the free
> energy in bulk water on one side of my membrane ion channel is about 30
> kcal/mol higher than bulk water on the other side of the channel. We think
> this discrepancy is due to other orthogonal degrees of freedom needing to
> be biased. We would like to add a bias to some of the dihedrals in this
> channel. I have my usual distanceZ colvar set for the center of mass of
> the channel and the center of mass of the ligand.
>
>
> Now, I am trying to add colvars for the dihedrals of four sidechains
> (channel is an homotetramer), the four histidine sidechains. That would be
> 5 colvars in my file. When I run the ABF, I get the error:
>
>
> FATAL ERROR: Memory allocation failed on processor 0
>
>
> If, I only do my distanceZ colvar and one of the dihedral colvars, then
> that error goes away, and then I get the error atom moving too fast...
>
>
> What is causing both of those errors? Can I not have multiple dihedral
> colvars in the same file?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>

-- 
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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