[gmx-users] Gromacs

[Justin Lemkul]

On 6/8/17 3:10 AM, saranya wrote:
> I have simulated the protein in water and protein with ligand for 100ns by
> using GPU and the edr file was generated using -rerun command on
> another system.I have just checked the pressure of my system by using
> gmx energy
> command, then i have selected pressure (group), but the calculated pressure
> is quite altered (20,000 pressure bar). Moreover, when I calculated the
> temperature of my system, the result was zero.

If you're recalculating energies from an .xtc, this is what you should expect. 
There are no velocities in an .xtc file so all properties related to kinetic 
energy (temperature and virial, hence pressure) are all garbage.

The original .edr file has these quantities.  You just can't use energygrps to 
decompose short-range nonbonded interaction energies on a GPU.  The other 
quantities are valid.

-Justin

> I have used below mdp file for the calculation
> title       = Protein-ligand complex NPT equilibration
> define      = -DPOSRES_LIG  ; position restrain the protein and ligand
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100       ; save coordinates every 100 ps
> nstvout     = 100       ; save velocities every 100 ps
> nstenergy   = 100       ; save energies every 100 ps
> nstlog      = 100       ; update log file every 100 ps
> energygrps  = Protein
> ; Bond parameters
> continuation    = yes           ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme = verlet
> ns_type     = grid      ; search neighboring grid cells
> nstlist     = 10         ; 10 fs
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein_EPI Water_and_ions    ; two coupling groups - more
> accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
> NPT
> pcoupltype  = isotropic                     ; uniform scaling of box vectors
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> compressibility = 4.5e-5                    ; isothermal compressibility of
> water, bar^-1
> refcoord_scaling    = com
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = no        ; velocity generation off after NVT
> 
> *With Regards,*
> 
> *Saranya Vasudevan,*
> 
> *Research Scholar,*
> 
> *Molecular Quantum Mechanics Laboratory,*
> 
> *Department of Physics,*
> 
> *Bharathiar University,*
> *Coimbatore-46*
> 

-- 
==================================================

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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