[gmx-users] Free energy change with harmonic restraints

[asaffarhi at post.tau.ac.il]

The equations in the articles are relevant for the step "Removal of  
Restraints" in that link.

Please note that these equations have been verified in

http://arxiv.org/abs/1501.01514

Best regards,
Asaf

Quoting hannes.loeffler at stfc.ac.uk:

> This may be of help:
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se  
> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of  
> Natalie Nguyen [nguyenn at wittenberg.edu]
> Sent: 09 July 2015 14:19
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Free energy change with harmonic restraints
>
> Dear Asaf,
>
> Thank you for the quick reply!
>
> I was wondering if it was possible to use thermodynamic integration  
> to represent growing harmonic restraints aside from using an  
> analytical method.
>
> I will cite this article most definitely!
>
> Natalie Nguyen
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se  
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of  
> asaffarhi at post.tau.ac.il <asaffarhi at post.tau.ac.il>
> Sent: Thursday, July 09, 2015 7:45 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Free energy change with harmonic restraints
>
> Dear Natalie,
>
> You have in
>
> http://xxx.tau.ac.il/pdf/1502.07196v3.pdf
>
> exact free energy of harmonic covalent bond and bond angle terms (or
> restrains). See Eqs. (2) and (3).
>
> There are also previous studies in the references there.
>
> For the dihedral term I assume it can also be calculated exactly (I
> might upload it).
>
> There is also to think if there are other contributions.
>
> If you are using it please cite.
>
> Best regards,
> Asaf
>
>
> Quoting Natalie Nguyen <nguyenn at wittenberg.edu>:
>
>> Dear all,
>>
>>
>> I am trying to measure the free energy change associated with
>> adding/removing harmonic restraints imposed on a ligand that is
>> attached to a protein. Is there any way to set this up?
>>
>>
>> Thank you ahead of time!
>>
>>
>> Natalie Nguyen
>> --
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