Re: analyzing NAMD trajectory with NAMD Energy

From: Markus Dahlgren (
Date: Mon Jul 29 2013 - 10:40:54 CDT

My question was wether the trajectory needed to be wrapped prior to
running NAMD energy. If I supply a dcd file and do not wrap/unwrap the
trajectory, am I supposed to get the correct analysis? Or does it need
to be unwrapped and then have the waters wrapped around the complex? I
do get different energies, but it is possible that the waters are not
wrapped perfectly around the complex using pbc tools.

I was mainly wondering if the wrapping is at all necessary if I supply a
xsc file for NAMD Energy and just process the dcd files output by NAMD?


On 7/29/2013 11:31 AM, Axel Kohlmeyer wrote:
> On Mon, Jul 29, 2013 at 5:13 PM, Markus Dahlgren
> <> wrote:
>> Hi,
>> Does a NAMD trajectory need to be wrapped/unwrapped prior to evaluation
>> using NAMD Energy? I get different energies depending on whether the
> how different?
> trajectory data is stored, read and processed inside of VMD with
> single precision floating point math and particularly for larger data
> sets, this can result in significant deviations due to truncation
> errors.
> in a single precision floating point number you have 23 bits for the
> mantissa. thus you can have the full resolution for coordinates where
> their magnitude lies between 1.0 and 2.0. for 2.0 and 4.0 you have
> half the resolution and thus lose one bit and similarly when you go to
> absolute coordinate positions of 8, 16, 32, 64, and 128 angstrom. at
> this point you lost 6 bits already and have 17 bits left and the
> granularity of position data is about 7.5e-6 almost two orders of
> magnitude larger than close to the origin.
> axel.
>> trajectory has been unwrapped prior to using NAMD Energy. Visually I can see
>> that parts of the protein-ligand complex has crossed the boundary border and
>> appears on the other side of the water box. Does the NAMD trajectory have
>> only the central image coordinates? Is wrapping not necessary for NAMD
>> Energy trajectory analysis when inputting NAMD trajectories? I have been
>> using NAMD
>> 2.8.
>> -Markus

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:29 CST