Re: [gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Hi Alex,

I thought by getting the flat-bottom restraint potential on my target molecule 
I should be able to get the free energy of unbiased case.
Basically; P(q)=P’(q)exp(V(q)/kBT) Here P is unbiased probability, P’ is biased 
probability and V is added potential.
However I am not totally sure. 

You can check http://plumed.github.io/doc-v2.2/user-doc/html/belfast-4.html 



On 17 Oct 2016, at 18:56, Alex  wrote:
> 
> Hi Gozde,
> 
> I also use something similar, by an simple pull restrain(distance) to keep
> a counter ion close to the charged molecule which is under perturbation in
> FEP.
> These type of restrains are \*Lambda  *independent and if I am not wrong
> their portion in free energy change should be calculated analytically by a
> formula like something you will see in below link in its "removal of
> restrains" section;
> 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> 
> But I have not been able to use it applicably, and I would be also
> appreciated if you could let me also know how to use if you find out either
> by this or ... .
> 
> Best regards,
> 
> Alex
> 
> On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin  wrote:
> 
>> Any idea?
>> Thanks.
>>> On 13 Oct 2016, at 15:42, gozde ergin  wrote:
>>> 
>>> Dear all,
>>> 
>>> I will use Gromacs to calculate the chemical potential difference of
>> solvation a surfactant molecule on the surface.
>>> System covers water molecules covered with surfactant molecules.
>>> I will apply flat-bottom restraint to the surfactant molecules in order
>> to stabilise them on surface. I will not let them to go inside the bulk.
>>> My question is how should I re-weight the free energy value to remove
>> the effect of flat-bottom restraint potential?
>>> 
>>> Thanks in advance.
>> 
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Re: [gmx-users] Thermodynamic integration and re-weighting method

[Alex]

Hi Gozde,

I also use something similar, by an simple pull restrain(distance) to keep
a counter ion close to the charged molecule which is under perturbation in
FEP.
These type of restrains are \*Lambda  *independent and if I am not wrong
their portion in free energy change should be calculated analytically by a
formula like something you will see in below link in its "removal of
restrains" section;

http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

But I have not been able to use it applicably, and I would be also
appreciated if you could let me also know how to use if you find out either
by this or ... .

Best regards,

Alex

On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin  wrote:

> Any idea?
> Thanks.
> > On 13 Oct 2016, at 15:42, gozde ergin  wrote:
> >
> > Dear all,
> >
> > I will use Gromacs to calculate the chemical potential difference of
> solvation a surfactant molecule on the surface.
> > System covers water molecules covered with surfactant molecules.
> > I will apply flat-bottom restraint to the surfactant molecules in order
> to stabilise them on surface. I will not let them to go inside the bulk.
> > My question is how should I re-weight the free energy value to remove
> the effect of flat-bottom restraint potential?
> >
> > Thanks in advance.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Any idea?
Thanks.
> On 13 Oct 2016, at 15:42, gozde ergin  wrote:
> 
> Dear all,
> 
> I will use Gromacs to calculate the chemical potential difference of 
> solvation a surfactant molecule on the surface.
> System covers water molecules covered with surfactant molecules.
> I will apply flat-bottom restraint to the surfactant molecules in order to 
> stabilise them on surface. I will not let them to go inside the bulk.
> My question is how should I re-weight the free energy value to remove the 
> effect of flat-bottom restraint potential?
> 
> Thanks in advance.

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[gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Dear all,

I will use Gromacs to calculate the chemical potential difference of solvation 
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to 
stabilise them on surface. I will not let them to go inside the bulk.
My question is how should I re-weight the free energy value to remove the 
effect of flat-bottom restraint potential?

Thanks in advance.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Dear all,

I will use Gromacs to calculate the chemical potential difference of solvation 
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to 
stabilise them on surface. I will not let them to go inside the bulk.
My question is how should I re-weight the free energy value to remove the 
effect of flat-bottom restraint potential?

Thanks in advance.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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