[gmx-users] PMF of large protein

[Jochen Hub]

>   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?  
>

I think it is difficult to estimate how quickly such a PMF converges, 
but probably extremely slowly. You would have to sample over all 
rotations of the protein which would rather take microseconds (or 
longer) than nanoseconds. The question is, how exact should the PMF be. 
Plusminus 1kcal (no chance to get there, I guess), or plusminus 5 kcal 
(difficult?), or 10 kcal (possible?)? The only way to find out is to 
try. You can do the complete umbrella sampling twice with *really 
independent* starting frames (e.g. different protein orientations) and 
check the difference between the PMFs.

Cheers,

Jcohen


>  
>
> 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?
>
>  
>
> 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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Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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