Re: analyzing NAMD trajectory with NAMD Energy

From: Axel Kohlmeyer (
Date: Mon Jul 29 2013 - 10:42:44 CDT

On Mon, Jul 29, 2013 at 5:40 PM, Markus Dahlgren
<> wrote:
> 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?

why don't you just try to answer the question that you were asked
instead of speculating.


> -Markus
> 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

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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