Re: Multiple Colvars

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Jul 25 2018 - 09:32:31 CDT

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Thanks Josh and Giacomo for the response. Giacomo, the 5-dimensional grid and checking the number of points went over my head. Could you clarify how I check this? Thanks!

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Tuesday, July 24, 2018 9:28:57 PM
To: NAMD list; McGuire, Kelly
Subject: Re: namd-l: Multiple Colvars

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<mailto: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?