[gmx-users] Gromacs under Windows

Cornel, J. J.Cornel at student.tue.nl
Sat Jan 24 12:41:00 CET 2004


I am running Gromacs under Windows 2000 and am reworking the MD course of RUG with the protein lysozyme. The pdb-file was succesfully converted into aki.top and aki.gro but when I try to generate the tpr-file with grompp I get the following error:

Back off! I just backed up mdout.mdp to ./#mdout.mdp.5#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling C:\Gromacs\bin\cpp...
processing topology...
processing coordinates...
Fatal error: number of coordinates on coordinate file <aki.gro,1555>
		does not match topology (aki.top,0>

But I am sure that these numbers are the same 1 protein of 1321 atoms and 78 water molecules (234) is together 1555.
I also downloaded the minim.mdp file in the MD course and adapted it to my windows system, at least I think I did. It looks likes this:

title		= Minimization of Hen Egg White Lysozyme (1AKI.pdb)	; Title of run

; The following lines tell the program the standard locations where to find certain files
cpp		= C:\Gromacs\bin\cpp	; Preprocessor
include		= C:\Gromacs\share\top\aki.top	; Directories to include in the topology format

; Parameters describing what to do, when to stop and what to save
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 1.0		; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps		= 200		; Maximum number of (minimization) steps to perform
nstenergy	= 10		; Write energies to disk every nstenergy steps
nstxtcout	= 10		; Write coordinates to disk every nstxtcout steps
xtc_grps	= Protein	; Which coordinate group(s) to write to disk
energygrps	= Protein	; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist		= 5		; Frequency to update the neighbor list and long range forces
ns_type		= simple	; Method to determine neighbor list (simple, grid)
rlist		= 1.0		; Cut-off for making neighbor list (short range forces)
coulombtype	= cut-off	; Treatment of long range electrostatic interactions
rcoulomb	= 1.0		; long range electrostatic cut-off
rvdw		= 1.0		; long range Van der Waals cut-off
constraints	= none		; Bond types to replace by constraints
pbc		= no		; Periodic Boundary Conditions (yes/no)

I hope you can help me because here in Eindhoven nobody works with Gromacs under windows, and consequently nobody can help me to solve the error!

Thanks in advance

kind regards

Jeroen Cornel

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