Hello everyone, I met with a problem today. I tried to simulate dppc lipid in water.However, when I want to minimize energy ,the grompp showed the error message like this: "number of coordinates in coordinate file (box.gro 8253 ) doesn't match topology ( topol.top , 0 ). I have used gromacs for sometime and checked the topology and itp file carefully , but can't find out the problem.can anyone help me ? here is the mdp file title = cpp = /lib/cpp -traditional-cpp include = none define = constraints = none ;h-bonds lincs_iter = 4
; RUN CONTROL PARAMETERS =
integrator = steep
tinit = 0
dt = 0.001 ; ps
nsteps = 6000
nstxtcout = 100 ; pos to xtc file
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
fourierspacing = 0.095 ; default to 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; ENERGY MINIMIZATION OPTIONS =
emtol = 100.0 ; default to 100
emstep = 0.02 ; default to 0.01
here is the topology file,and I have added the ffgmx forcefield into
"lipid1.itp"
#include "lipid1.itp"
#include "dppc.itp"
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 SOL OW 1 -0.82 15.99940
2 HW 1 SOL HW1 1 0.41 1.00800
3 HW 1 SOL HW2 1 0.41 1.00800
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
[ system ]
; name
DSPC in water
[ molecules ]
; name number
DSP 64
SOL 1599
em.mdp
Description: Binary data
topol.top
Description: Binary data
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