[gmx-users] error after grompp

[Nur Syafiqah Abdul Ghani]

Hi all,

I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
below :

Fatal error:
Atom 410 in multiple T-Coupling groups (1 and 2)

Actually I do not understand what the error said even when i'm Google
it to forum there was no one
facing like mine..Here i put together my topology and the nvt.mdp.
Hope you can give me some idea that i cant see.

Another question,why is in the nvt.mdp at the temperature coupling
there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u
explain it why?

topology :

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "metal_Protein_chain_A.itp"

; Include position restraint for protein
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif

; Include ion chain topologies
#include "metal_Ion_chain_A2.itp"

; Include position restraint for metal
#ifdef POSRES_ION
#include "posre_Ion_chain_A2.itp"
#endif

; Include water topology
#include "gromos53a6.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos53a6.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Ion_chain_A2        1
SOL         8780
NA               1


nvt.mdp :

title       = Protein-ligand complex NVT equilibration
cpp             = /usr/bin/cpp
include         = -I/usr/share/gromacs/top
define      = -DPOSRES  ; position restrain the protein and ligand
; 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
energygrps  = Protein ZN
; 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     = 10        ; 10 fs
rlist       = 1.4       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4       ; 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
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_ZN Water_and_ions    ; 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
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 for your help in advance,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulghani at gmail.com @ GS33669 at mutiara.upm.edu.my