[gmx-users] MD run error

[David van der Spoel]

Mahalakshmi S wrote:
> Dear All,
> 
> I am a newbie to gromacs.
> I am trying to do a MD simulation for 2ns at constant temperature of 
> 298K and a constant pressure of 1atm. Temperature and pressure were 
> regulated by weak coupling to an external bath and electrostatics was 
> dealt by using a 8angstrom Coulombic cut-off. I fully solvated the 
> structure with SPC water in a cubic box with a 20 angstrom edge length. 
> I did energy minimization for the structure using steepest descents for 
> 1000 steps and a position restrained MD run. I want the system to 
> eveolve according to Newton's equation of motion, with equations being 
> integrated every 2fs. I am trying to do a full MD and I am getting 
> error. I am attaching the full.mdp file. Below you would find the errors 
> which I got. Please let me know whats wrong wit my full.mdp or how could 
> I correct this error.
> 
> I executed this command :
> 
> grompp -v -f full.mdp -o full.tpr -c after_pr.grp -p ubq.top.
> 
> It gives me the following error :
>  reating statusfile for 1 node...
>  Sorry couldn't backup mdout.mdp to ./#mdout.mdp.2#
>  WARNING 1 [file full.mdp, line unknown]:
>   Unknown left-hand warnings in parameter file
> 
> checking input for internal consistency...
> calling /usr/bin/cpp...
> sh: gromppmMKf08: No such file or directory
> cpp exit code: 256
> Tried to execute: '/usr/bin/cpp  -I/usr/local/share/gromacs/top  ubq.top >
> gromppmMKf08'
> The '/usr/bin/cpp' command is defined in the .mdp file

This is the problem, find the location of the cpp command on your system 
and replace the line in the mdp file.

> processing topology...
> Cleaning up temporary file gromppmMKf08
> Fatal error: Could not open gromppmMKf08
> 
> Thanks,
> Lakshmi
> 
> 
> ------------------------------------------------------------------------
> 
> title= ubq
> warnings = 10
> cpp = /usr/bin/cpp
> integrator = md
> dt = 0.002
> nsteps = 1000000
> nstcomm = 1
> nstxout = 250
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ; Neighbour Searching
> ns_type = grid
> ; Electrostatics and VdW
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.8
> rvdw = 0.9
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1 
> tc-grps = protein sol
> ref_t = 298  298
> ; Pressure coupling is on
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-05
> ref_p = 1.0
> ; Generate velocities is on at 300 K.
> gen_vel = yes
> gen_temp = 298.0
> gen_seed = 173529
> constraints = all-bonds
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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