From: Hemanth Vemuri (hemanthvemuri1997_at_gmail.com)
Date: Thu Jun 22 2017 - 01:34:15 CDT
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
>
>
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