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

Sampo Karkola sampo.karkola at helsinki.fi
Thu Mar 22 15:31:29 CET 2007

Thanks for the quick answer!

I did gmxcheck for the em and md tpr-files and they do differ on lot of 
things. However, I do not know what these differences mean. I was 
looking for some documentation about the output from gmxcheck but 
couldn't find any, so if someone has some guides on how to read the 
output, I'd be grateful. Or if someone would be kind enough to take a 
look at the output at http://www.helsinki.fi/~karkola/gmxcheck.tar.gz



Mark Abraham wrote:
> 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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