Re: use of colvars to restrain the absolute positions of all atoms in a large system

From: Abir Ganguly (7.someone.iitd_at_gmail.com)
Date: Wed Jul 10 2013 - 12:11:10 CDT

Hi Jerome,

Thanks a lot for the reply. I will look into the RMSD colvar variable. I am also going through a tutorial from Dr. Chris Chipot in which the use of such colvars are illustrated.

Also, if it is not too much trouble, I would like to know how to calculate the restraint free energy from the NAMD in-built restraints. I will appreciate if you can direct me to a place where such calculations are described.

Thanks,

Abir
On Jul 10, 2013, at 5:07 AM, Jrme Hnin wrote:

> Hi Abir,
>
> You may obtain the same effect as positional restraints within the colvars by restraining a RMSD variable, for which you disable the least-squares fit process (thus calculating the raw, unfitted RMSD instead of the minimal RMSD). This, however, will incur a performance penalty compared with NAMD's built-in positional restraints ("harmonic constraints", which badly need to be renamed).
>
> Conversely, there are ways you can calculate the restraint free energy, even for NAMD's built-in restraints, through post-processing of the trajectory: it is very easy to calculate the restraint forces on each atom, and then you have a choice of several estimators for the free energy.
>
> Finally, given what you are trying to accomplish, I am not convinced that restraining all atoms in the system is a good idea.
>
> Cheers,
> Jerome
>
>
> ----- Original Message -----
>> Hi Giacomo and Aron,
>>
>> Thanks for the suggestions.
>>
>> I am using the alchemical simulations implemented in NAMD to
>> calculate the free energy difference for a particular
>> transformation. However, due to hysteresis related issues, I need to
>> perform this transformation in steps. One of the steps is to
>> calculate the loss of configurational entropy associated with the
>> process of putting these restraints on all the atoms. The next step
>> would be to calculate the free energy change for a process within
>> this restrained system.
>>
>> Hence, the reason for using the colvars (and not constraints) is
>> because we would like to obtain the free energy of the process as we
>> slowly remove the restraints.
>>
>> We will still be doing dynamics because we are restraining the atoms,
>> and not constraining ( or freezing) them.
>>
>> In other words, the goal is to restrict the ribozyme to only local
>> motions, and find out the cost related to that in terms of free
>> energy.
>>
>> I hope I am not too confusing.
>>
>> Thanks,
>>
>> Abir
>>
>>
>>
>> On 07/09/2013 05:16 PM, Giacomo Fiorin wrote:
>>
>>
>> Hello Abir, you can use the colvars module to restrain the center of
>> mass of your protein to stay near the dummy, so that the protein
>> doesn't drift while its internal dynamics is unaffected. This may be
>> helpful for you to visualize the trajectory, but the FEP calculation
>> doesn't require it.
>>
>>
>> If you want to restrain each atom individually, that requires
>> defining a variable for each atom, which in the end defeats the
>> purpose of defining "collective" variables?
>>
>> The most efficient way to apply restraints atom-by-atom is still the
>> "constraints" keyword: what is the reason why you can't use it?
>>
>>
>> Giacomo
>>
>>
>>
>> On Tue, Jul 9, 2013 at 6:01 PM, Abir Ganguly <
>> 7.someone.iitd_at_gmail.com > wrote:
>>
>>
>> Hi NAMD users,
>>
>> I have a very specific question regarding the use of the colvars
>> module that I am stating below.
>>
>> I am trying to use the colvars module to restrain the absolute
>> positions of all the atoms in my system, which is a ribozyme. I am
>> running some alchemical FEP simulations on the system and I need to
>> fix(restrain) the positions of all these atoms during the
>> simulations.
>>
>> I can not use the constraints option in NAMD because of reasons that
>> I can state later, if required.
>>
>> I realize that I can define a dummy atom, and can use the 'distance'
>> option in colvar to harmonically restrain the position of all atoms
>> to that dummy atom. I was curious what would be a clean and smart
>> way to go about it, since I have so many atoms. It will be really
>> helpful if there are some templates with these sort of colvars, so
>> that I can get some directions as to how to build my input file.
>>
>> Thanks,
>>
>> Abir
>>
>>
>>
>>

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