[gmx-users] confusion on NPT MD simulation

[Ming Tang]

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?

Thanks in advance.



-----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 Ming Tang
Sent: Monday, 15 June 2015 6:05 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] confusion on NPT MD simulation

Dear Justin,

I got a problem making me confused for weeks.
I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them?
As you mentioned,  freezing and pressure coupling are incompatible. My first understanding was that I cannot fix atoms during NPT. Therefore, I have been steering my collagen in NVT recently.  After minimization, I equilibrated my collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, and then stretched it using pull code. Do you think this simple process can give a good starting point for SMD?

Thanks very 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> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Monday, 1 June 2015 9:46 PM
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] confusion on NPT MD simulation



On 6/1/15 4:40 AM, Ming Tang wrote:
> Dear gromacs experts,
>
> I tried to equilibrate a triple helix using NPT, and the .mdp file is like this:
>
> DEFINE           =  -DPOSRES
> integrator       =  md
> dt               =  0.0009
> nsteps           =  1000000
> nstxout          =  0
> nstvout          =  0
> nstlog           =  10000
> nstxtcout        =  10000
> xtc-precision    =  10
> cutoff-scheme    =  verlet
> coulombtype      =  reaction-field-zero
> coulomb-modifier =  potential-shift-verlet rcoulomb-switch  =  0.8
> rcoulomb         =  1.4
> epsilon_r        =  15
> vdw-modifier     =  force-switch
> rvdw-switch      =  0.8
> rvdw             =  1.4
> tcoupl           =  v-rescale
> tc-grps          =  Protein non-protein
> tau-t            =  1.0 1.0
> ref-t            =  310 310
> Pcoupl           =  parrinello-Rahman
> Pcoupltype       =  isotropic
> tau-p            =  5
> compressibility  =  3e-4
> ref-p            =  1.0
> refcoord_scaling =  all
> pbc              =  xyz
> freezegrps       =  C
> freezedim        =  Y Y Y
>
> C is a group containing atoms of both the first and the last residues in all the three chains.
> But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation?
> Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed.  I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate.
>

Freezing and pressure coupling are incompatible; see notes in the manual.

-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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

==================================================
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