[gmx-users] confusion on NPT MD simulation

[Justin Lemkul]

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

-- 
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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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