[gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Thu Mar 22 15:40:49 CET 2007

Hi Sampo,

I don't know if this is obvious to you but when you start a simulation from
a energy-minimized configuration you should use

*grompp -t minimization.trr -c minimization_out.gro* (here you will use a
full-precision configuration)

and not only

*grompp -c minimization_out.gro*  (in contrast, here you will have a
configuration with rounding errors)

It seems that your system is far from trivial and has to be very well
energy-minimized before starting an MD run.

Regards,

Pedro.

2007/3/22, Mark Abraham <Mark.Abraham at anu.edu.au>:
>
> Sampo Karkola wrote:
> > Dear list,
>
> Thanks for the good problem description!
>
> > I am trying to simulate a crystal structure of a protein with a cofactor
> > (NADP, I've used NDPP topology) and a (self-made) ligand in a box of
> > water. The preparation of the simulation went normally: pdb2gmx,
> > editconf, genbox, grompp (for ions), genion, grompp (for em) mdrun (em),
> > grompp (for md), mdrun (md). Now, in the md simulation, the potential
> > and total energies of the system rise immediately from the beginning,
> > stabilize to a certain level and later the run crashed with LINCS
> > warnings. Earlier I have succesfully simulated a model of an another
> > enzyme with similar procedure and in that run the potential energy
> > decreased immediately and stabilized with no crashes. I tried to
> > simulate the protein alone, the cofactor alone and the ligand alone and
> > the energies rise in all cases.
> >
> > Luckily, I had an older simulation (with gromacs 3.2.1, now I'm using
> > 3.3.1) with the same ligand (except one atom type is changed from NR in
> > the old topology to N in new topology) alone and there the energies
> > decreased as they should. To study the differences in the ligand-alone
> > simulations, I performed an mdrun with the old tpr file (mdrun -s
> > old.tpr -o new_run -c new_run...) and the energies decreased again, as
> > they should. Next, I grompped a new tpr-file from the old gro, top and
> > mdp files, got a new tpr file and simulated it resulting in decreasing
> > energies again. But when I try to do the whole process from the
> > beginning using the same pdb file as in the older run something goes
> > differently and the mdrun produces rising energies. The energy
> > minimisation with the new run takes over 3000 steps while the old run
> > was minimised in 34 steps. I've checked that the gro and top files
> > between the old (working) and the new (non-working) runs are identical.
>
> So far everything looks good to me.
>
> > The only differences I find are in the tpr files of the energy
> > minimisation and md simulation and they look like this (compared with
> > diff):
>
> gmxcheck -s1 old.tpr -s2 new.tpr is the recommended way to check for
> this sort of thing.
>
> > 22983c22983
> > <             atom[     4]={type=  2, typeB=  2, ptype=    Atom, m=
> > 1.40067e+01, q= 4.80000e-02, mB= 1.40067e+01, qB= 4.80000e-02, resnr=
> >  0} grpnrs=[ 0 0 0 0 0 0 0
> >  0 0 0 ]}
> > ---
> >  >             atom[     4]={type=  1, typeB=  1, ptype=    Atom, m=
> > 1.40067e+01, q= 4.80000e-02, mB= 1.40067e+01, qB= 4.80000e-02, resnr=
> >  0} grpnrs=[ 0 0 0 0 0 0 0
> >  0 0 0 ]}
> > 22985c22985
> > plus a lot of these atom definitions.
>
> These seem strange to me - the "type" values in the above arrays should
> be indices into an atomtype array earlier in the .tpr file, but if the
> above values are right, and the two atoms 4 should correspond, then the
> atomtype array should also be different... but diff is not reporting
> this, and I do not understand why. Does gmxcheck differ? (Recall that
> this is not the fourth atom, since numbering starts at zero).
>
> > plus a lot more coordination, velocity, atom type and interaction
> > definitions.
>
> Evidently, since the starting configuration is embedded in the .tpr and
> the endpoint of the previous minimization was different.
>
> > I have no dihedral restraints applied and those sc_power, dihre-fc and
> > scalepower definitions are different even in the old, working simulation
> > and in the one which was grompped again and producing correct results
> > with decreasing energies.
> >
> > So the problem is that the old gro, top and mdp files give correct
> > results even with grompped again, but a new procedure starting from the
> > pdb file give bad results.
> >
> > I was hoping that someone could direct me to the correct direction and
> > find out what's wrong. All suggestions are highly appreciated and
> tested!
>
> Not much joy from me, I'm afraid!
>
> Mark
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