[gmx-users] Nvt T-coupling error

[Poncho Arvayo Zatarain]

I`m
running a simulation of dppe+dppe+ligand+wáter and i`m building
index with the command gmc make_ndx –f minimiz-gro –o index.ndx.
When i use the command the following options appears to build the
index:
0
System    27592 atoms
1
Other      27592 atoms
2
LIG
                8 atoms
3
DPPC          8320 atoms
4
DPPE          7744 atoms
5
TIP3          11520 atoms




And
i selected 3|
4 | 2 | 5 and creates the group DPPC_DPPE_LIG_TIP3
with 27592 atoms. Then i used the command instruction gmx
grompp -f nvt.mdp -c minimiz.gro -p dppc+dppe+ligand+water.top -n
index.ndx -o nvt.tpr, i run it and the following error appears: Fatal
error: 11520 atoms are not part of any of the T-coupling groups. Could anybody help me to solve the error please? My nvt.mdp is the following:
title		= NVT equilibration for DPPC-DPPE-LIGANDdefine		= -DPOSRES	; position restrain the protein; Run parametersintegrator	= md		; leap-frog integratornsteps		= 50000		; 2 * 50000 = 100 psdt		    = 0.002		; 2 fs; Output controlnstxout		= 100		; save coordinates every 0.2 psnstvout		= 100		; save velocities every 0.2 psnstenergy	= 100		; save energies every 0.2 psnstlog		= 100		; update log file every 0.2 ps; Bond parameterscontinuation	= no		    ; first dynamics runconstraint_algorithm = lincs	; holonomic constraints constraints	= all-bonds	        ; all bonds (even heavy atom-H bonds) constrainedlincs_iter	= 1		            ; accuracy of LINCSlincs_order	= 4		            ; also related to accuracy; Neighborsearchingns_type		= grid		; search neighboring grid celsnstlist		= 5		    ; 10 fsrlist		= 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); Electrostaticscoulombtype	= PME		; Particle Mesh Ewald for long-range electrostaticspme_order	= 4		    ; cubic interpolationfourierspacing	= 0.16		; grid spacing for FFT; Temperature coupling is ontcoupl		= V-rescale	            ; modified Berendsen thermostattc-grps		= DPPC DPPE    LIG  	    ; three coupling groups - more accuratetau_t		= 0.1	0.1	0.1   	    ; time constant, in psref_t		= 303 	303	303         ; reference temperature, one for each group, in K; Pressure coupling is offpcoupl		= no 		; no pressure coupling in NVT; Periodic boundary conditionspbc		    = xyz		; 3-D PBC; Dispersion correctionDispCorr	= EnerPres	; account for cut-off vdW scheme; Velocity generationgen_vel		= yes		; assign velocities from Maxwell distributiongen_temp	= 323		; temperature for Maxwell distributiongen_seed	= -1		; generate a random seed; COM motion removal; These options remove motion of the protein/bilayer relative to the solvent/ionsnstcomm		= 1comm-mode	= Linearcomm-grps	= DPPC_DPPE LIG