[gmx-users] a basic question

Yang Ye leafyoung at yahoo.com
Sat Aug 11 06:14:33 CEST 2007


Why you put a none in the include? It doesn't mean none when there is an
"none".

Regards,
Yang Ye

On 8/11/2007 11:36 AM, Q733 wrote:
> 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
>
> ------------------------------------------------------------------------
>
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