# Re: PMF calculations between membrane and nano particle simulations

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Thu Jul 03 2014 - 17:46:24 CDT

Hi Giacomo Florin,
given in user guide (under 10.2.2 Collective variable components) makes me
confusion.

Hear is the description :

In certain conditions, distanceZ can also be periodic, namely when periodic
boundary conditions (PBCs) are defined in the simulation and distanceZ's
axis is parallel to a unit cell vector. The following keywords can be used
within periodic components (and are illegal elsewhere):

* period < (distanceZ) Period of the component >
Acceptable Values: positive decimal
Default Value: 0.0
Description: Setting this number enables the treatment of distanceZ as a
periodic component: by default, distanceZ is not considered periodic. The
keyword is supported, but irrelevant within dihedral or spinAngle, because
their period is always 360 degrees.

Internally, all differences between two values of a periodic colvar follow
the minimum image convention: they are calculated based on the two periodic
images that are closest to each other.

In certain conditions, distanceZ can also be periodic, namely when periodic
boundary conditions (PBCs) are defined in the simulation and distanceZ's
axis is parallel to a unit cell vector.

In my namd config file, I have given the box information and distanceZ
colvar input file also I provided (as mentioned previous mail). So
according to this description it is periodic colvar.

period < (distanceZ) Period of the component >
Acceptable Values: positive decimal
Default Value: 0.0
Description: Setting this number enables the treatment of distanceZ as a
periodic component: by default, distanceZ is not considered periodic.

I did not specify the period in my colvar input file, so it will take
default value 0.0. according to this description, it might not be periodic
colvar.

It makes me confuse to know that the colvar is periodic or not.

Thanks,
Subbu.

On Fri, Jul 4, 2014 at 3:04 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hi Subbu, no, there won't be problems if the particle drifts in x and y,
> because only the z component of the distance vector is being used.
>
> Cheers
> Giacomo
>

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