[gmx-users] constraint pull code / gromacs 5.0.4

[CARDELLINI ANNALISA]

Dear Justin,
thank you for your email.
As you guessed, my mdp file was related to one indipendent 
window.

>What is atypical is the application of a constraint 
>rather than a harmonic potential.  The typical "umbrella" 
>in "umbrella sampling."

I have already tried to use the typical "umbrella" in 
"umbrella sampling" and then WHAM algorothm for the PMF, 
but I had some problem to set the right spring constant in 
each window. I didn't have idea how to chose k 
constant.The PMF changed according to the k constant. Do 
you have some suggestions to get independent results from 
"k"?
Moreover, I got a PMF characterized by high oscillations, 
do you have idea why?

My system is made of 2 nanoparticles of Alumina in water.

Thank you very much
Annalisa


On Tue, 23 Jun 2015 16:17:42 -0400
  Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> On 6/23/15 2:10 PM, Alex wrote:
>> The pulling rate, as it appears in your mdp, is actually 
>>zero. That aside,
> 
> ...which is correct if one is sampling independent 
>windows and collecting the forces to reconstruct the PMF.
> 
> What is atypical is the application of a constraint 
>rather than a harmonic potential.  The typical "umbrella" 
>in "umbrella sampling."
> 
>> we do not have enough info about the system. What are 
>>the nanoparticles
>> made of? What forcefield is being used? Can you use 
>>trjconv to see what's
>> going on?
>> Please check that your system is happy prior to pulling. 
>>The huge variation
>> in forces could mean weird pulling behavior (which does 
>>happen), or that
>> your particles are "breathing." Set constraints to 
>>'none' and pull code to
>> see if your system behaves. The use of constraints 
>>should be deprecated in
>> general, but I fear for my life suggesting it here.
> 
> It's dangerous to make broad generalizations like 
>"constraints should be deprecated."  Sometimes 
>constraints are not appropriate (materials, crystals, 
>etc).  But for the vast majority of biomolecular 
>simulations, we really don't care about different 
>vibrational states of bonds involving H, so there's zero 
>purpose to running our simulations 4x slower just to 
>collect information we don't need :)
> 
> -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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Annalisa Cardellini, M.Sc.
Ph.D. student

Politecnico di Torino - Energy Department
Corso Duca degli Abruzzi, 24
10129 Turin - ITALY
Tel: +39-011-090-4495
Fax: +39-011-090-4499

E-mail: annalisa.cardellini at polito.it
SMaLL: http://www.polito.it/small