[gmx-users] NVT simulations for poylsaccharides in CHARMM36

[Justin Lemkul]

On 7/17/17 9:22 AM, Jivesh Madan wrote:
> I was doing NVT simulations on a structure constituting of 3 monomers of
> AGLC residue(glucose molecule) connected via 1-4 linkage.
> Though I have modified my nvt.mdp file for CHARMM36 but still encountering
> errors.

Your vdW treatment is incorrect and you should not be applying any long-range 
correction.

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

> The following is the nvt.mdp and I am also attaching the topology file
> topol.top with it.
> 
> 
> define = -DPOSRES ; position restrain the protein
> ; 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 0.2 ps
> nstvout = 100 ; save velocities every 0.2 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 ps
> ; removing CM translation and rotation
> ;comm_mode       =  ANGULAR
> ;nstcomm         =  1
> ; Bond parameters
> continuation = no ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> dwtype         = cutoff
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.2
> rlistlong       = 1.2
> rvdw-switch     = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; 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 = Berendsen ; modified Berendsen thermostat
> tc-grps = System Non-Protein ; two coupling groups - more accurate
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 330 330 ; 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 = 330 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
> cutoff-scheme = Verlet
> 
> 
> 
> These are the errors which I am facing
> 
> NOTE 1 [file nvt.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
> 
> Setting the LD random seed to 2905043056
> Generated 85052 of the 85078 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 55198 of the 85078 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Other'
> turning H bonds into constraints...
> Setting gen_seed to 475227507
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
> 
> WARNING 1 [file topol.top, line 699]:
>    The bond in molecule-type Other between atoms 3 O1 and 4 A1 has an
>    estimated oscillational period of 9.1e-03 ps, which is less than 5 times
>    the time step of 2.0e-03 ps.
>    Maybe you forgot to change the constraints mdp option.
> 
> Analysing residue names:
> There are:     3      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> 
> -------------------------------------------------------
> Program gmx, VERSION 5.0.2
> Source code file:
> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/readir.c,
> line: 3205
> 
> Fatal error:
> Invalid T coupling input: 3 groups, 1 ref-t values and 1 tau-t values
> 

This error is inconsistent with what you posted above.  Please provide your 
actual .mdp file if you want commentary on how to fix the problem.  But the 
error is pretty plain - you can't specify three groups and only have one set of 
thermostat parameters.  Each group needs corresponding values.

-Justin

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

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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