From: Niklaus Johner (nij2003_at_med.cornell.edu)
Date: Thu Mar 01 2012 - 14:52:24 CST
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
>
>
>
>
>
>
>
>
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