# Re: Defining custom Colvars to measure pmf with Umbrella Sampling

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jun 22 2017 - 09:15:21 CDT

Hello Hemanth, Brian's suggestion was both useful and pretty clearly
explained:

1) apply a bias to a variable that is already implemented and you're sure
of its definition;
2) extract a PMF by WHAM or other method along the collective variable
"number of Hemanth's waters", where the definition and computation is
entirely under your control.

Applying a harmonic restraint and measuring a probabilistic PMF do not need
to be done on the same variable.

Giacomo

On Thu, Jun 22, 2017 at 2:34 AM, Hemanth Vemuri <hemanthvemuri1997_at_gmail.com
> wrote:

> Brian,
> What i meant was that i did not find a suitable collective variable
> components on which i can apply harmonic biasing method to run Umbrella
> sampling. I did not understand what you meant by saying "you just count the
> number of waters that meet your criterion", are there any other collective
> variable components that help us do this? since i am new to namd and MD
> simulations, it would be very helpful if you could point me to some
> resources regarding this.
> I referred to this (http://www.ks.uiuc.edu/Training/Tutorials/science/
> channel/channel-tut.pdf) tutorial to run Umbrella sampling in namd
>
> Thanks for advice,
>
> Hemanth Vemuri,
> undergraduate student
> Center for Computational Natural Sciences and Bioinformatics,
> International Institute of Information Technology,
> Gachibowli, Hyderabad 500 032
> Telangana, India
>
> On Wed, Jun 21, 2017 at 9:46 PM, Radak, Brian K <bradak_at_anl.gov> wrote:
>
>> This does not make sense to me - there is very much a collective variable
>> to describe the number of waters as a reaction coordinate - you just count
>> the number of waters that meet your criterion. Whether or not you can apply
>> a bias to this coordinate is a different question, but this does not seem
>> to be what you are asking.
>>
>>
>> Your question seems more related to analysis than simulation setup using
>> NAMD or colvars. Am I misunderstanding?
>>
>>
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
>> brian.radak_at_anl.gov
>> ------------------------------
>> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
>> Hemanth Vemuri <hemanthvemuri1997_at_gmail.com>
>> *Sent:* Tuesday, June 20, 2017 12:25:29 AM
>> *To:* namd-l_at_ks.uiuc.edu
>> *Subject:* namd-l: Defining custom Colvars to measure pmf with Umbrella
>> Sampling
>>
>> Hello,
>> My goal is to measure the changes in pmf as we vary the number of water
>> molecules inside/around(1) a protein. But the problem i am facing is that
>> there is no suitable colvars which will help me achieve this, like for
>> example if i want to measure pmf with radius of gyration as the reaction
>> coordinate , there is already Rg collective variable which i can specify in
>> the colvars input file, but there is no colvar with which i can measure the
>> pmf with number of water as a reaction coordindate. Hence i wanted to know
>> if there is a way with which i can define a custom collective variable or
>> is there any other way to reach my goal.
>>
>> (1) - I call these waters as penetrated waters and am defining them as
>> waters belonging to contact water which are not within 3 angstrom of bulk
>> water.
>> Contact water are defined as water within 3.5 angstrom of protein and the
>> water which are not contact water are defined as bulk water.
>>
>> Thanks for advice
>>
>> Hemanth Vemuri,
>> undergraduate student
>> Center for Computational Natural Sciences and Bioinformatics,
>> International Institute of Information Technology,
>> Gachibowli, Hyderabad 500 032
>> Telangana, India
>>
>>
>

```--
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
```

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