[gmx-users] (no subject)

[Justin Lemkul]

On 12/7/15 12:30 AM, Seera Suryanarayana wrote:
> Dear Gromacs Users,
>
> Sorry for the same mail again. I haven't provide sufficient information in
> previous mail.
>
> After energy minimization I have done nvt equilibrium for 1ns. It has taken
> 15 to 20 minutes when I done it previously. Same equilibrium I did day
> before yesterday and it has take almost one day. I have used the same work
> station in both equilibrium processes. I have used the following mdp file.
> System consists 129 residue length protein and more the three 3,00,000
> water molecules. Kindly check the mdp file and let me how to resolve this
> long lasting processes.
>
> I have used the following command:
> mdrun -deffnm nvt -nt 4          means one MPI thread and 4 openMPP
> threads.
>
> topol.top info:
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> SOL         300217
> NA               11
>

You have a system of nearly 1 million(!) atoms.  For a 129-aa protein, this is 
wildly unnecessary unless the polypeptide is fully unfolded.  Is this the case? 
I would also never expect a run done on 4 cores, without a GPU, to ever achieve 
such performance like you claim above. Such a system will take many days to run 
on such hardware, not 15 minutes.

-Justin

>
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 500000                ; 2 * 500000 = 1000 ps
> dt                  = 0.002             ; 2 fs
> ; Output control
> nstxout         = 5000          ; save coordinates every 10.0 ps
> nstvout         = 5000          ; save velocities every 10.0 ps
> nstenergy       = 5000          ; save energies every 10.0 ps
> nstlog          = 5000          ; update log file every 10.0 ps
> ; Bond parameters
> continuation            = no            ; 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                ; 20 fs, largely irrelevant with
> Verlet
> rcoulomb            = 1.0               ; short-range electrostatic cutoff
> (in nm)
> rvdw                = 1.0               ; short-range van der Waals 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 is on
> tcoupl          = V-rescale                 ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; 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 is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz               ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
>
> Thanks in advance
> Surya
> Graduate student
> India.
>

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

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

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