Re: cellBasisvectors/.xsc fixing/colvars while running amber ff

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 21 2011 - 17:06:43 CDT

Hi Francesco, cell basis vectors or an xsc file should always be specified,
regardless of force field. There are no specific configurations for PBC
when running with colvars, periodic image wrapping is controlled only in the
output routines to DCD and .coor files.

How are your wrapAll and wrapWater keywords?

Giacomo

On Fri, Oct 21, 2011 at 2:13 PM, Francesco Pietra <chiendarret_at_gmail.com>wrote:

> Hello:
> I am running parm7 amber files with namd 2.8 cuda for a protein
> complex in a rectangular box, TIP3PBOX water. After heating to 310K,
> at the first pressure equilibration with protein complex atoms fixed,
> and commented out cellBasisvectors ( xsc file specified), I notice
> unusually many water molecules out of the box. Only 25,000 steps,
> timestep 1fs, were carried out.
>
> Question: should, when running amber ff, the cellBasisVectors be
> always specified? Is the answer the same when colvars are applied in
> place of fixing atoms?
>
> thanks
> francesco pietra
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:55 CST