[gmx-users] Fatal Error: number of coordinates in coordinate file does not match topology

[Chitrita Dutta Roy]

I want to perform MD Equilibration run under position restrained for
200ps. Bond
distances were constrained using the LINCS (Linear Constraints) algorithm,
the water molecules were restrained using the SETTLE algorithm. In order to
do this I have modified nsteps in original pr.mdp file. Following is the
modified file contents:



;

; User spoel (236)

; Wed Nov 3 17:12:44 1993

; Input file

;

title = Yo

cpp = /usr/bin/cpp

define = -DPOSRES

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 100000 ; total 200 ps.

nstcomm = 1

nstxout = 50

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 10

ns_type = grid

rlist = 1.0

rcoulomb = 1.0

rvdw = 1.0

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein SOL

tau_t = 0.1 0.1

ref_t = 300 300

; Energy monitoring

energygrps = Protein SOL

; Pressure coupling is not on

Pcoupl = no

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is on at 300 K.

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529



Then I wanted to do grompp with this modified pr.mdp file. But it is showing
a Fatal error like,

Fatal Error:

number of coordinates in coordinate file does not match topology.

But if I use the original pr.mdp (without modifying it for 200ps) the grompp
runs properly. I am not understanding what to do now. Please help me out.

Thanking you,

Chitrita.
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