[gmx-users] confusion on NPT MD simulation

[Tsjerk Wassenaar]

Hi Ming Tang,

You don't need a huge force constant to keep it fixed. Too high forces may
give instabilities. And a more gentle one (100-1000) does the trick as well.

Cheers,

Tsjerk
On Jun 17, 2015 4:17 AM, "Ming Tang" <m21.tang at qut.edu.au> wrote:

> Dear Justin,
>
> Thank you so much.  There are another 2 papers in which the authors said
> they equilibrated their  collagen like this. This really made me confused
> for quite a  long time, and I come to you for help finally. Critical
> analysis is important.
>
> In the "steps to perform a simulation" page, step 8  indicates that NPT
> equilibration is for fixing the density. I have been confused about how
> should I equilibrate my collagen before SMD simulation. I  want to keep the
> shape (do not change its length) of my collagen during equilibration, so
> that the force-deformation curve will not be changed because of the
> equilibration process. After knowing that freezing and pressure coupling is
> incompatible, I tried to use NVT with heavy atoms restrained by using
> -DPOSRES, and further the simulation to SMD (actually umbrella and
> direction-periodic are used) directly in NVT. The simulation run smoothly
> and I got my force-deformation curve, but I am still concerned whether my
> equilibration is good enough for SMD simulation, and whether the results
> are credible.
> If I choose to further equilibrate my collagen in NPT after in NVT, is it
> feasible to restrain parts (backbone, terminal atoms) of my collagen by
> adding a huge force constant (say 1*10e6  kJ/mol/nm^2) through -fc in
> genrestr command, so that its shape will be reserved during the
> equilibration?
>
> Could you please kindly give me some guidance on which is the best
> equilibration process I show follow to get a good starting point for SMD
> (umbrella+direction-periodic) simulation?
>
> Thank you so much.
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> Sent: Tuesday, 16 June 2015 9:37 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] confusion on NPT MD simulation
>
>
>
> On 6/16/15 5:27 AM, Ming Tang wrote:
> > Dear Justin,
> >
> > I read a paper, in which the author equilibrated the collagen like this:
> > Firstly, a 100 ps NVT MD simulation at a temperature 310 K was
> > performed, in which velocity rescaling algorithm with 1ps coupling
> > constant was used. Rigid bonds were used to constraint covalent bond
> > length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble
> > with 1bar pressure was used to equilibrate the system while keeping
> > the temperature at 310 K, where Berendsen barostat with 1ps coupling
> > constant was adopted. In this step, the whole protein was held fixed.
> > Lastly, we further equilibrated the system in a NPT ensemble for
> > 400ps, with a more accurate pressure coupling algorithm based on
> > Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first
> and the last C − α atoms of each chain were constrained.
> >
> > I wonder whether they used genrestr to restrain atoms, like utilising
> > -fc to add a quite large force in all directions to them, and
> > considered those atoms are kept fixed during NPT equilibration?
> >
>
> People are often lazy (or inconsistent) with language.  Holding something
> "fixed" might mean "huge restraint" or it might actually mean frozen
> (freezegrps in the .mdp).  There are functional differences between these
> two.  Atoms are also not "constrained" (that's a restraint!) in GROMACS, so
> there may be some loose language here...
>
> If you have questions about methods for published work relevant to what
> you're doing, that's what corresponding authors are for!
>
> -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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