Re: colvar restraint simulation

From: Prabir Khatua (prabir07chem_at_gmail.com)
Date: Mon Feb 25 2019 - 13:52:39 CST

Hi Josh and Fiorin,

Thanks for the reply. There is no problem in the simulation itself.
However, I was not obtaining the expected result. Thus, I was concerned
whether defined force constant
was properly applied so that I can get an idea to tune this value in order
to obtain expected result after looking at the data. I had a concept that
total force constant gets
multiplied if multiple force constants are defined in a single harmonic
block in the following way

harmonic {
        colvars d1 d2
        centers 3.5 3.5
       force constant 5.0 5.0
}

That is why I was wondering whether the same was the case in my case or not
although I defined those in two different harmonic blocks.

Sincerely,

Prabir

On Mon, Feb 25, 2019 at 11:40 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hi Prabir, the documentation is here:
>
> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic
>
> The restraints that you define will only be applied to the selected
> variables, i.e. 5 and 1 respectively. Check, however, for typos, because
> you have a couple.
>
> Giacomo
>
> On Mon, Feb 25, 2019 at 12:08 PM Prabir Khatua <prabir07chem_at_gmail.com>
> wrote:
>
>> Hi NAMD users,
>>
>> I want to do a distance restraint simulation where I need to use
>> different force constants
>> for different distance variables. I am using the following configuration
>> file
>>
>> colvar {
>> name d1
>> distance {
>> group1 { atomNumbers 3608} # A6 I31:O
>> group2 { atomNumbers 566} # A1 V39:N
>>
>> }
>> }
>>
>> colvar {
>> name d2
>> distance {
>> group1 { atomNumbers 2462}
>> group2 { atomNumbers 2963}
>>
>> }
>> }
>>
>> colvar {
>> name d3
>> distance {
>> group1 { atomNumbers 2439}
>> group2 { atomNumbers 3106}
>>
>> }
>> }
>>
>> harmonic {
>> colvars d1 d2
>> centers 3.5 3.5
>> force constant 5.0
>> }
>>
>> harmonic{
>> colvars d3
>> centers 4.0
>> force constant 1.0
>> }
>>
>> I am wondering whether simulation will apply a force constant of 5.0 on
>> d1 and d2, while
>> 1.0 on d3. Please let me know if I am doing wrong and suggest me how to
>> do it.
>> Any suggestion would be appreciated.
>>
>> Thanks,
>>
>> Prabir
>>
>> *Prabir Khatua*
>> *Postdoctoral Research Associate*
>> *Department of Chemistry & Biochemistry*
>> *University of Oklahoma*
>> *Norman, Oklahoma 73019*
>> *U. S. A.*
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

-- 
*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*

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