Re: PMF calculations between membrane and nano particle simulations

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jul 07 2014 - 18:05:06 CDT

Hello Subbarao, the value of distanceZ is being calculated using PBCs, and
more precisely the minimum image convention. For the code, this does not
make it a periodic variable, only a variable whose values are limited to an
interval as long as the box length.

You could instruct the code that this is a periodic variable, for example
if you to enable a moving restraint that crosses the simulation box
multiple times (similarly to rotating a torsional angle multiple times).
 But that's really not necessary in your case.

If your simulation is not unstable but you only see the nanoparticle
jumping around in VMD, there is likely no problem with your protocol, just
the usual confusion about PBCs that has been discussed many times.

Giacomo

On Thu, Jul 3, 2014 at 6:46 PM, Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:

> Hi Giacomo Florin,
> Thank you for your reply but the description
> 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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