From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Dec 17 2020 - 08:38:08 CST
Hello Aashish, please copy the list in your reply.
Can you please clarify what is the problem?
On Thu, Dec 17, 2020 at 9:26 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in>
wrote:
> Dear Sir
>
> Your assumption is correct.
> My group1 atoms are 20Å far from the group2 atoms.
> I have performed 10000 steps minimisation and the equilibration with
> solvent for 500ps.
> In the solvent equilibration, I have constrained the solute then performed
> ABF dynamics (NVT).
> During ABF simulation Group1 atoms are going inside the cyclodextrin
> molecule after the very first frame. Although, I want to perform a
> simulation for the formation of the inclusion complex at 6 windows
> instead of at the first window.
> Can you please tell me if there is any way to modulate the process?
> I have attached the colvar file with this mail.
> I have applied the 5kcal/mol/Å2 restrained force on the cyclodextrin
> (glycosidic oxygen).
>
>
> Best regards
>
> Aashish
>
>
> On Sat, Dec 12, 2020 at 8:48 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Asshish, you didn't say which type of variable (function) you used.
>> Assuming that you used a "distance" function:
>>
>> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distance
>> you are defining indeed the distance between the two COMs.
>>
>> Specifically, the "program" that computes the COMs of groups is actually
>> NAMD, while Colvars uses them to define the collective variable and the
>> biasing forces on it that allow you enhanced sampling and PMF computation.
>> (Instead, other types of collective variables that are not based on COMs
>> are computed entirely within Colvars.)
>>
>> In your publication, you should therefore cite both the NAMD and Colvars
>> papers:
>> https://doi.org/10.1063/5.0014475
>> https://doi.org/10.1080/00268976.2013.813594
>>
>> Thanks,
>> Giacomo
>>
>> On Sat, Dec 12, 2020 at 3:18 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in>
>> wrote:
>>
>>> Dear Sir
>>>
>>> I have a system with cyclodextrin and peptide. I want to study the
>>> formation of the inclusion complex via the adaptive biasing force method.
>>> As discussed in the following paper.
>>> DOI: 10.1039/c7cp02292a
>>> I took the group 1 colvar glycosidic bond oxygen atoms and in another
>>> group 2 selection of heavy atoms of the N terminal or C-terminal amino acid
>>> residue.
>>> I want to know whether the program automatically calculates the COM or I
>>> have to give a different format.
>>>
>>>
>>> Best regards
>>>
>>> Aashish
>>>
>>>
>>>
>>>
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