[gmx-users] PMF of large protein

[Justin A. Lemkul]

Matteus Lindgren wrote:
> Dear all,
> 
>  
> 
> I will try to calculate PMF with gromacs for the first time and I have 
> some basic questions regarding this.
> 
>  
> 
> I will calculate the PMF of moving a relatively large protein (700 
> residues) through water a distance of 2nm towards a perfectly flat TiO2 
> surface in order to estimate the interaction between the protein and the 
> surface and the effect of modifications of the mineral surface. The 
> total system is around 120 000 atoms and I can run about 4ns per day. My 
> first question is simply: is it practically possible to run a number of 
> PMF calculations of the protein movement for such a large system? 
>  According to tutorials, sampling at every 0.1nm is sufficient so 20 
> points*sampling time ~1 ns = 20ns which could be ok but then there is 
> not time to allow for much protein rotation. Opinions about this?  
> 
>  

If you're referring to the tutorial linked from the Gromacs site, please note 
that those distances were found to be acceptable for that particular system, and 
may not be generalizable to all systems.  Further, 1 ns of sampling in each 
window probably isn't enough for very large systems.

> 
> My second question concerns the pull code. I understand how to use the 
> umbrella sampling and g_wham to calculate PMF but how is constraint 
> pulling used? Pros and cons?
> 

Constraint pulling can be used for SMD (generating a series of initial 
configurations) or for calculation of PMF, although not with WHAM.  There was a 
post about this a day or two ago; see the archives.

-Justin

>  
> 
> Thank you
> 
> Matteus
> 
> --------------------------------------------------------- 
> 
> Matteus Lindgren, graduate student
> Department of Chemistry, Umeå University
> SE-901 87 Umeå, Sweden
> Phone:  +46 (0)90-7865368 
> 
>  
> 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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