[gmx-users] PMF calculation with constraint distance

[leila salimi]

Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I
want to do the same with gromacs to have some knowledge  about my FF
parameters and compare with my DFT results!
You meant I have to do with different configuration and average the forces?
I am wondering that I did in DFT for each constrained distances around 15
ps MD and then I used averaged forces for each distances!

Cheers,
Leila

On Thu, May 21, 2015 at 11:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/21/15 5:00 PM, leila salimi wrote:
>
>> Hi all,
>>
>> I started to calculate PMF between two ions in solution and I
>> used constraint for pull option, instead of umbrella as I saw in Umbrella
>> sampling Tutorial of Justin.
>>
>> This is the part of my mdp file!
>> ; Pull code
>> pull            = constraint    ; Justin's value was "umbrella"
>> pull_geometry   = distance      ; simple distance increase
>> pull_dim        = Y Y Y
>> pull_start      = no            ; Justin's value was "yes"
>> pull_ngroups    = 1
>> pull_group0     = CA_surf
>> pull_group1     = carboxylate_carbon
>> pull_init1      = 0.288         ; initial distance between pulling groups
>> pull_rate1      = 0.001 ; 0.001 nm per ps
>> pull_k1         = 1000          ; kJ mol^-1 nm^-2
>>
>> I got the output  and I tried to pull out with increasing  the distance
>> between two atoms and I have pullf.xvg file!
>>
>> I know that I can have the time evolution of constrained distance with
>> g_dist from xtc file! I am wondering how to have the distance with
>> corresponding constrained force?
>> If I have the file contain forces and distances, I can integrate the force
>> then I will have PMF.
>>
>>
> This probably won't give you a very reliable PMF.  You're effectively
> trying to use the Jarzynski method (albeit with a constraint rather than a
> harmonic potential) with one run (normally you have to do this many, many
> times), which won't give a correct result.
>
>  Could you help me that how I can manage this?
>>
>
> If you have the constraint force in pullf.xvg and the distance in another
> .xvg file, it's just a matter of using grep/awk to combine the two.
> Whether or not this means anything is another matter.  Getting a PMF
> between ions is trivially simple with a harmonic potential.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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