[gmx-users] Charmm 36 forcefield with verlet cut-off scheme

[akk5r]

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
------------------------------------------------------- 

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