[gmx-users] Re: freeze the particular residues in NPT-NVT

[라지브간디]

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Thanks for your mail Justin.


I encountered the another problem after i didn't delete the whole part (protein, system, non-prptein..etc) in index.ndx file.


Fatal error:
37872 atoms are not part of any of the T-Coupling groups
 
These are my NVT.mdp file :
title		        = OPLS Lysozyme NVT equilibration define		= -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 cellsnstlist		= 5		; 10 fsrlist		= 1.0		; short-range neighborlist cutoff (in nm)rcoulomb	= 1.0		; short-range electrostatic cutoff (in nm)rvdw		= 1.0		; 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		= Protein Non-Protein	; two coupling groups - more accuratetau_t		= 0.1 0.1		; time constant, in psref_t		= 300 300 		; 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	= 300		; temperature for Maxwell distributiongen_seed	= -1		; generate a random seedfreezegrps      = g1 g2 g3 g4 g5 g6 g7 g8 g9 g10 g11 g12 g13 g14 g15 g16 g17 g18 g19 g20 g21 g22 g23 g24 g25 g26 g27 g28 g29    freezedim       =  Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y 






> Dear gmx, 
> 
> 
> I have used freezgreps for 20 residues of 152 residues contained protein 
> and the it took well for energy minimization steps according to the input 
> given on mdp and index files. However, when i go for further NPT steps it 
> gives following error. 
> 
> 
> Fatal error: 
> Group Protein referenced in the .mdp file was not found in the index file. 
> Group names must match either [moleculetype] names or custom index group 
> names, in which case you must supply an index file to the '-n' option 
> of grompp. 
> 
> 
> I have rechecked the reference structure (em.gro) with index and nvt.mdp 
> files but all of their index numbers are correct. can anyone tell me how 
> would avoid them? Thanks in advance. 
> 
> 
The "Protein" group is a default group and should always be present. The 
only reason I can think of that would cause this is if you created an index 
file and then deleted the Protein group from it. If grompp receives an 
index file on the command line, the groups provided therein supersede 
default groups.