Re: we apply a harmonic potential

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jun 10 2019 - 12:38:36 CDT

Hello Jiali, please reply to the whole list, so that everyone can benefit
from the conversation.

Regarding wrapAll, the following section explains how PBC wrapping affects
results:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar_atom_groups_wrapping

Regarding your starting configuration, you have a force constant of 60
kcal/mol and the initial snapshot is 4 Å away from the restraint center,
thus the initial restraint energy is 1/2*60*4^2 = 480 kcal/mol. It is up
to you to decide if this is appropriate for your system.

Giacomo

On Mon, Jun 10, 2019 at 1:31 PM Jiali Wang <jwang204_at_binghamton.edu> wrote:

> HI Giacomo,
> Thank you so much for your help. what I want to do is sampling a CLA
> passway, this can't happened in cMD, initial distance is about 20A, i use
> center 16A as first try. But umbrella sampling is not working, calculation
> is faster than usual, and all energy output is NAN, I attach the output
> file. could you please help me with this problem? By the way, is that
> necessary to turn off wrapAll in simulation?
> best,
> Jiali
>
> On Sun, Jun 9, 2019 at 4:19 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hello Jiali, the block that you used is sufficient to define a harmonic
>> restraint. If you run multiple independent simulations each with a
>> different restraint center, you are doing umbrella sampling. But it
>> requires that you set suitable initial conditions for each window.
>>
>> targetCenters is used to change the restraint centers over time, and run
>> the windows sequentially. It is one (but not the only) way to set up
>> initial conditions for each window. You will probably also want
>> targetNumStages to define how many windows.
>>
>> For details, see here:
>>
>> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic
>>
>> On Sun, Jun 9, 2019 at 2:34 PM Jiali Wang <jwang204_at_binghamton.edu>
>> wrote:
>>
>>> Dear Giacomo,
>>> I am confusing when setting a umbrella sampling,in colvar file of
>>> harmonic part, I set as following:
>>> harmonic {
>>> name lenpot
>>> colvars length
>>> centers 5.0
>>> forceConstant 60.0
>>> }
>>> But I found tutorials mention need to set a target center,
>>> targetCenters 1.0
>>> targetNumSteps 2000000
>>> What I understand umbrella method is sampling ligand from center
>>> distance to target distance,by apply a harmonic potential, is
>>> that correct? If I don't set targetcenter, what's is this sampling means?
>>> Thank you for your help and your time!!
>>> best,
>>> Jiali
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Research collaborator, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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