[gmx-users] confusion on NPT MD simulation

[Ming Tang]

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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