[gmx-users] Isn't dt=0.0001 very small?

[Diego Enry Gomes]

Hi Andrew, I have just repeated this tutorial. There is nothing wrong  
with that.

Download all the files again and repeat the tutorial from the beginning.
It can be a file that was corrupted during your previous download or  
you did something wrong in one of the steps.

You can copy&paste the following lines to your terminal. Sit down and  
relax.
If that doesn't work you have a problem with your gromacs installation.


#start copy

wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/1LYD.pdb
wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/em.mdp
wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/pr.mdp
wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/run.mdp

#run the whole thing
echo 5 | pdb2gmx -f 1LYD.pdb -water tip3p
editconf -f conf.gro –bt dodecahedron –d 0.5 –o box.gro
genbox_d -cs -cp box.gro -p topol.top -o solvated.gro
grompp -v -f em.mdp -c solvated.gro -p topol.top -o em
mdrun -v -deffnm em
grompp -v -f pr.mdp -c em.gro -t em.trr -p topol.top -o pr
mdrun -v -deffnm pr
grompp -v -f run.mdp -c pr.gro -t pr.trr -p topol.top -o md
mdrun -v -deffnm md

#end copy



Diego.

--
=========================================
Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA.  +1 (509) 372.6363
diegoenry.gomes at pnl.gov
=========================================

On Mar 10, 2009, at 12:36 AM, Andrew Voronkov wrote:

> Dear GROMACS users,
> I'm doing this tutorial:
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
> and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during  
> equilibration. It works only with dt=0.0001 which seems very very  
> small step for me. Is it ok or I need to clean up the warnings like  
> in error below(it's for dt=0.002):
>
> starting mdrun 'T4-*LYPOZYME in water'
> 25000 steps,     50.0 ps.
> Warning: 1-4 interaction between 2 and 20 at distance 2.619 which is  
> larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> t = 0.000 ps: Water molecule starting at atom 100062 can not be  
> settled.
> Check for bad contacts and/or reduce the timestep.
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
> Wrote pdb files with previous and current coordinates
> step 0Segmentation fault
> andrew at linux-f29d:~/GROMACS_MD/1LYD>
>
> Here is pr.mdp:
>
> integrator = md
> nsteps = 25000
> dt = 0.001
> nstlist = 10
> rlist = 1.0
> coulombtype = pme
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> tcoupl = Berendsen
> tc-grps = protein non-protein
> tau-t = 0.1 0.1
> ref-t = 298 298
> Pcoupl = Berendsen
> tau-p = 1.0
> compressibility = 5e-5 5e-5 5e-5 0 0 0
> ref-p = 1.0
> nstenergy = 100
> define = -DPOSRES
>
>
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