Re: How to calculate free energy to unbias colvars restraint?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Jul 29 2017 - 09:51:01 CDT

I mean using the coorfile command:
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node9.html#SECTION00052200000000000000

On Fri, Jul 28, 2017 at 8:17 PM, Victoria Lim <limvt_at_uci.edu> wrote:

> Giacomo, when you say to re-run the unbiased trajectory through NAMD, does
> that mean an additional simulation? Can you expand further on how to do
> that?
>
> Thanks,
> Ria
>
> On Fri, Jul 28, 2017 at 5:10 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> You could try free-energy perturbation, but the two states (restraint on
>> / restraint off) are probably quite different and convergence may be poor.
>> An option could be switching the force constant gradually:
>> http://colvars.github.io/colvars-refman-namd/colvars-refman-
>> namd.html#x1-770006.4.3
>> (Note the comment in the description.)
>>
>> From the technical point of view, you can always re-run the unbiased
>> trajectory through NAMD to evaluate the energy of Colvars or any additional
>> energy terms that weren't included originally.
>>
>> Giacomo
>>
>> On Fri, Jul 28, 2017 at 7:56 PM:
>>
>>> Dear NAMD users,
>>>
>>> I have a molecular dynamics simulation employing a harmonic distance
>>> restraint using the colvars module in NAMD. I am looking for a way to
>>> calculate the free energy of removing the restraint so that I can correct
>>> data from the calculations using the restraint. Is there a way I can
>>> re-evaluate the energies of a stored trajectory with the restraints turned
>>> off?
>>>
>>> Thank you!
>>> Ria
>>>
>>
>>
>>
>> --
>> 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
>>
>
>

-- 
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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