[gmx-users] a basic question

[Yulia Einav]

I had exactly this problem. The reason was I've edited mdp file at
Windows. Sounds silly, I know, but just do your editing for mdp at
Linux, it solved the problem for me.

 

Yulia Einav Ph.D. 

 

 

________________________________

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Q733
Sent: Saturday, August 11, 2007 5:36 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] a basic question

 

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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