Re: Internal Unit system

From: Victor Ovchinnikov (ovchinnv_at_georgetown.edu)
Date: Thu Mar 01 2012 - 15:16:00 CST

The units are AKMA
http://www.charmm.org/documentation/c34b1/usage.html#%20AKMA
PDBVELFACTOR should correspond to the conversion from AKMA inverse time
to inverse picoseconds

sqrt ( 4184 (J/kcal) * 10^20 (Ang/m)^2 * 1000 (g/kg) ) * 10 ^ (-12)
(s/ps)

Victor

On Thu, 2012-03-01 at 15:52 -0500, Niklaus Johner wrote:
> Thanks for the answer, but from what I understand these are the
> input/output units, not the internal units used in namd.
> Indeed it is stated in the user guide section on input/output
> (http://www.ks.uiuc.edu/Research/namd/2.8/ug/node13.html):
>
>
> "Velocities in DCD files are stored in NAMD internal units and must be
> multiplied by PDBVELFACTOR=20.45482706 to convert to Å/ps"
>
>
> suggesting that either the length or time unit used internally in namd
> is something weird. Moreover, kcal/mol, Angstroms and Bars are not
> consistent units (Energy/Distance^3 is not equal to Pressure).
>
>
> Thanks,
>
>
> Niklaus
>
> Niklaus Johner
> Weill Cornell Medical College
> Harel Weinstein Lab
> Department of Physiology and Biophysics
> 1300 York Avenue, Room D-501
> New York, NY 10065
>
>
>
>
>
>
>
>
>
>
>
>
> On Mar 1, 2012, at 1:14 PM, Ajasja Ljubetič wrote:
>
> > It says in the user guide:
> > "The standard units used by NAMD are Angstroms for length, kcal/mol
> > for energy, Kelvin for temperature, and bar for pressure. Wallclock
> > or CPU times are given in seconds unless otherwise noted."
> > http://www.ks.uiuc.edu/Research/namd/2.8/ug/node13.html
> >
> >
> > Mass is in atomic units and charge (at least in the CHARMM force
> > field) in multiples of the elementary charge.
> >
> >
> > Best regards,
> > Ajasja
> >
> > On Thu, Mar 1, 2012 at 18:21, Niklaus Johner
> > <nij2003_at_med.cornell.edu> wrote:
> > Dear NAMD users,
> >
> >
> > I am trying to find out what the internal units in namd are.
> > I need the information because I am using the PLUMED plugin
> > which uses these units in its input files. I couldn't find a
> > definite answer anywhere. I guess the units stated in
> > section 3.2.3 of the user manual are not the units used
> > internally (they are not consistent).
> >
> >
> > From what I could gather (PDBVELFACTOR and TIMEFACTOR) it
> > seems that the length unit is [0.997 Angstrom] and the time
> > unit is [48.8 fs]. Is that right? And what about the other
> > units (mass, temperature, charge)? A table with the units in
> > the user guide would be welcome.
> >
> >
> > Thanks!
> >
> >
> > Niklaus
> >
> > Niklaus Johner
> > Weill Cornell Medical College
> > Harel Weinstein Lab
> > Department of Physiology and Biophysics
> > 1300 York Avenue, Room D-501
> > New York, NY 10065
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:16 CST