Re: Multiple Colvars

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jul 24 2018 - 22:28:57 CDT

You definitely can. Check, however, whether what you are requesting is a
5-dimensional grid, and estimate the number of points. Multiply this by 8,
and you get the number of bytes needed.

On Tue, Jul 24, 2018 at 4:39 PM McGuire, Kelly <mcg05004_at_byui.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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