[gmx-users] Warning/Error message in NVT & NPT

[Mark Abraham]

On Mon, Feb 18, 2013 at 5:24 AM, Wui Zhuan Lim <wuizhuanl at hotmail.com>wrote:

>
> Hi all,
>
> I'm a beginner in using Gromacs and MD simulation works.
> I am currently doing a simulation of enzyme unfolding.
> When I began NVT equilibration, a warning note appeared, as shown below:
> With twin range cut-offs and SHAKE the virial and pressure are incorrect.
> At first, I tried to ignore the warning with -maxwarn (although it's
> better not to use it, just have a try)
> The warning did disappear.
> As
>  I move forward to NPT, the same message appeared again. But it's no
> longer "warning", but "error" instead, which cannot be avoided with
> -maxwarn, so I could not proceed NPT at the moment.
> So I was
> wondering if it's a serious issue to fix it. I understand what twin
> range cut-offs and SHAKE are, but how will I know the appropriate virial
>  and pressure?
>

If a combination of algorithms isn't implemented and there's an error that
prevents it, then the GROMACS authors were serious about it :-) What
GROMACS version is this? Why are you using SHAKE rather than LINCS?

Also note that your PME parameters are very crude, and that re-generating
velocities when you start NPT is generally not what you want to do.

Mark


>
> Regards,
> Adam
>
> **Below are my mdp files for NVT and NPT:
>
> NVT
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES
> ; Run parameters
> integrator  = sd
> nsteps      = 10000
> dt          = 0.002
> ; Output control
> nstxout     = 100
> nstvout     = 100
> nstenergy   = 100
> nstlog      = 100
> energygrps  = Protein Non-Protein
> ; Bond parameters
> continuation    = no
> constraint_algorithm = shake
> constraints     = hbonds
> ; Neighborsearching
> ns_type     = grid
> nstlist     = 5
> rlist       = 0.9
> rcoulomb    = 0.9
> rvdw        = 1.4
> ; Electrostatics
> coulombtype     = PME
> pme_order       = 3
> fourierspacing  = 0.16
> ; Temperature coupling
> tc_grps     = Protein Water_and_ions
> tau_t       = 0.1   0.1
> ref_t       = 300   300
> ; Pressure coupling
> pcoupl      = no
> ; Periodic boundary conditions
> pbc         = xyz
> ; Dispersion correction
> DispCorr    = EnerPres
> ; Velocity generation
> gen_vel     = yes
> gen_temp    = 300
> gen_seed    = -1
>
>
>
> NPT
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES
> ; Run parameters
> integrator  = sd
> ld_seed     = -1
> nsteps      = 2500000
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100
> nstvout     = 100
> nstenergy   = 100
> nstlog      = 100
> energygrps  = Protein Non-Protein
> ; Bond parameters
> continuation    = no
> constraint_algorithm = shake
> constraints     = hbonds
> shake_tol       = 0.0000001
> ; Neighborsearching
> ns_type     = grid
> nstlist     = 5
> rlist       = 0.9
> rcoulomb    = 0.9
> rvdw        = 1.4
> ; Electrostatics
> coulombtype     = PME
> pme_order       = 3
> fourierspacing  = 0.16
> ; Temperature coupling
> tc_grps     = Protein Water_and_ions
> tau_t       = 0.1   0.1
> ref_t       = 300   300
> ; Pressure coupling
> pcoupl      = Berendsen
> pcoupltype  = isotropic
> tau_p       = 2.0
> ref_p       = 1.0
> compressibility = 4.5e-5
> refcoord_scaling    = com
> ; Periodic boundary conditions
> pbc         = xyz
> ; Dispersion correction
> DispCorr    = EnerPres
> ; Velocity generation
> gen_vel     = yes
> gen_temp    = 300
> gen_seed    = -1
>                                           --
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