[gmx-users] issues running virus capsid simulation

[Justin Lemkul]

On 9/24/19 5:09 PM, Asis Jana wrote:
> Hi,
>
> I am doing viral capsid simulation using GROMACS 2018. The capsid was first
> energy minimized using the steepest-descent algorithm followed by 40 ns of
> NVT (300 K) followed by 10 ns of NPT (300 K, 1 atm) equilibration. In the
> NVT and NPT equilibration, the heavy atoms of the protein were restrained
> with a force constant of 1000 kJ/mol/nm. Production MD simulations were
> performed for 400 ns at a temperature of 300 K and a pressure of 1 atm.
> Please see the production mdp file below.
>
> title           = MD simulation
> ; Run parameters
> integrator      = md
> nsteps          = 2000000000
> dt                  = 0.002
> ; Output control
> nstxout                 = 50000
> nstvout                 = 50000
> nstenergy               = 50000
> nstlog                  = 50000
> nstxout-compressed  = 50000
>
> compressed-x-grps   = System
>
> continuation            = yes
> constraint_algorithm    = lincs
> constraints                 = h-bonds
> lincs_iter                  = 1
> lincs_order                 = 4
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type             = grid
> nstlist                 = 20
> rlist                   = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> pme_order           = 4
> fourierspacing  = 0.16
> ; Temperature coupling is on
> tcoupl          = Nose-Hoover
> tc-grps         = Protein Non-Protein
> tau_t           = 1.0     1.0
> ref_t           = 300     300
> ; Pressure coupling is on
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = isotropic
> tau_p                   = 5.0
> ref_p                   = 1.0
> compressibility     = 4.5e-5
> 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 is off
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = Protein Non-Protein
>
> I have attached RMSD and Rg plots with this mail. It looks like that capsid
> is stiil not equilibrated. Rg is increasing rapidly, whereas RMSD of the
> capsid is increasing slowly. Please see the attached plots.  Any kind of
> advice or suggestions are deeply appreciated.

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What do your eyes tell you when you visualize the trajectory? Do the 
data make sense? Have you accounted for periodicity effects? Are there 
simply structural changes happening? Nothing says any structural metric 
has to level off in some convenient amount of time.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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