**From:** Ioana Cozmuta (*ioana_at_nas.nasa.gov*)

**Date:** Sat Jan 10 2004 - 18:24:18 CST

**Next message:**Jérôme Hénin: "Dihedral restraint"**Previous message:**AMIT PALIWAL: "Interaction energy for fixed atoms"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi namd users,

I am not sure about the following.

Say I use a value of 0.001 for the SMD velocity. The manual says that the

unit corresponding to this velocity is Angstroms/timestep.

The timestep in the MD simulations is 1fs however I print the output in

the SMD every 100 steps. So is the velocity

1. Angstroms/fs

2. Angstroms/(fs*100)

I would say that the first answer is the correct one.

Assuming that the velocity is expressed in Angstroms/timestep of MD

integration, I want then

to calculate the work using the formula in the tutorial on the NAMD web

site

W=v*dt*cumsum(f)

I use here v=0.1A/ps, dt=0.1 ps (I print the output every 100 steps).

However in the SMD I also have the r_CM of the SMD atoms output at every

step, thus I could also calculate

W=sum[del_r_cm*f]

The two values are however different (there is one order of magnitude

difference between the two values).

Any comment?

Thanks,

Ioana

**Next message:**Jérôme Hénin: "Dihedral restraint"**Previous message:**AMIT PALIWAL: "Interaction energy for fixed atoms"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:37:17 CST
*