On 9/19/13 2:21 PM, akk5r wrote:
Hey All,
I am running a simulation of a POPC bilayer in water using a Charmm 36
forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt
equilibration.
My .mdp file is as follows:
title = OPLS Lysozyme NVT equilibration
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 = 0 ; save coordinates every 0.2 ps
nstvout = 0 ; save velocities every 0.2 ps
nstenergy = 0 ; save energies every 0.2 ps
nstlog = 0 ; update log file every 0.2 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
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.2 ; 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)
rcoulomb-switch = 0
rvdw-switch = 1.0
; long-range cut-off for switched potentials
rlistlong = 1.4
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = POPC SOL ; 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 = No ; account for cut-off vdW scheme
; Method for doing Van der Waals
vdw-type = switch
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
cutoff-scheme = Verlet
*Here is the output when I run grompp to make the .tpr file:*
grompp -f nvt.mdp -c em_POPC.gro -p topol.top -o nvt.tpr
ERROR 1 [file nvt.mdp]:
With Verlet lists only cut-off LJ interactions are supported
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.
NOTE 2 [file nvt.mdp]:
The switch/shift interaction settings are just for compatibility; you
will get better performance from applying potential modifiers to your
interactions!
Generated 21528 of the 21528 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 18355 of the 21528 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Setting gen_seed to 7358
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
There were 2 notes
-------------------------------------------------------
Program grompp, VERSION 4.6.1
Source code file: /home/ali/Downloads/gromacs-4.6.1/src/kernel/grompp.c,
line: 1593
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
As the error message says, with "cutoff-scheme = Verlet" you must use "vdwtype =
cutoff." The notes above suggest reasonable methods for implementing switched
interactions.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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