From: Aashish Bhatt (aashish.ph16221_at_inst.ac.in)
Date: Thu Dec 17 2020 - 23:07:59 CST
Thank you for the information sir
On Thu, Dec 17, 2020 at 8:49 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Once again, please keep the list in CC. Sharing this information is the
> primary reason why the list exists in the first place.
>
> It is hard to make a good guess about the process without having access to
> your data (i.e. without being you).
>
> You have defined wall restraints at the boundaries of each window. First,
> be aware of the following:
> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_config_changes
> and perhaps consider making them explicit harmonicWalls restraints.
>
> Second, those restraints ought to work if the distance is computed
> correctly. Does the value of that distance make sense to you when you look
> at the trajectory? Look into the role of PBCs:
>
> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar_atom_groups_wrapping
>
> On Thu, Dec 17, 2020 at 9:53 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in>
> wrote:
>
>> Dear sir,
>>
>> I want to perform the simulation of the formation of inclusion complex in
>> six windows i.e, I want to move the peptide towards the cyclodextrin cavity
>> by 5Å in each window(Total 30 Å).
>>
>> But in my case, the whole process is getting completed within the first
>> window.
>>
>> Herein I am pasting my colvar input file.
>>
>> Best regards
>>
>>
>> colvarsTrajFrequency 100
>> colvarsRestartFrequency 1000
>>
>> colvar {
>> name COMDistance
>>
>> width 0.1
>>
>> lowerboundary -20.0
>> upperboundary -15.0
>>
>> lowerwallconstant 10.0
>> upperwallconstant 10.0
>>
>> distance {
>> group1 {
>> atomnumbers { 148 149 150 151 152 155 157 159 160 161 162 163
>> 165 167 169 171 } ## Peptide atoms
>> }
>> group2 {
>> atomnumbers { 21 42 63 84 105 126 147 } ## Cyclodextrin
>> }
>> }
>> }
>>
>> abf {
>> colvars COMDistance
>> fullSamples 500
>>
>> On Thu, Dec 17, 2020 at 8:08 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> wrote:
>>
>>> 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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