Re: applying harmonic constraints in cphmd

From: Brian Radak (
Date: Sat Nov 20 2021 - 10:25:31 CST

This is unfortunately an unsolved problem. As you point out - the atom
indices change during a CpHMD simulation and so the selections would
need to be updated at each cycle (probably with a bit of bookkeeping).
One thing that can be exploited is that the number of residues does not
change, so if it is possible to use residue and name based selections,
that should work.

In previous work where we used restraints we took advantage of the fact
that it was only a single residue that was titrating and so all indices
above the atom sidechain are fixed during the simulation (a bit of a hack).

To be honest, it might be easier for someone to implement restraints
based on a selection syntax rather than solve the indexing problem that
is specific to CpHMD.



On 11/20/21 12:29 AM, Diship Srivastava wrote:
> Hi,
> I am currently working on insertion of an antimicrobial peptide (AMP)
> on bilayer membrane using constant pH MD. I am trying to constrain the
> center of mass of AMP and membrane, while cphmd is active. Since cphmd
> doesn't have colvar support and number of atoms during cphmd changes
> during the run, both colvars and constraints result in fatal error
> during the job. How can I constrain the com under cphmd conditions?
> Thanks in advance.
> --
> Diship Srivastava
> Department of Chemistry
> IIT(ISM) - Dhanbad
> India

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST