Re: PMF calculations between membrane and nano particle simulations

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Tue Jul 08 2014 - 01:01:15 CDT

Hi Giacomo,
                    Tank you for your valuable explanation.
Thanks,
Subbarao kanchi.
On 8 Jul 2014 04:35, "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com> wrote:

> 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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