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

Sampo Karkola sampo.karkola at helsinki.fi
Fri Mar 23 08:23:44 CET 2007


Hi Tsjerk and Mark,

thanks for the answers.

The topologies differ in one atom which is changed from NR in the old 
topology to N in new topology and also, there is one dihedral angle not 
defined in the old topology and then zero is used by grompp. In the new 
topology, the dihedral is defined as an improper one to keep the atoms 
in plane. I did a test run where I changed that particular dihedral to 
correspond to the old working topology but the results are the same, 
i.e. energies rising.

About the energy minimisations in vacuum, I have not performed them when 
using gromacs 3.2.1, and I have upgraded to 3.3.1 so I can't compare. I 
really do not feel like installing 3.2.1 again :)

It's not only the ligand. Also the protein itself (17beta-HSD, pdb code 
1fdt) and the cofactor (NADP+, NDPP topology from ffG43a1.rtp) give 
these rising energies when simulated alone, so I do not think that the 
error is in the top files, as mentioned by Mark. But you are welcome to 
take a look at http://www.helsinki.fi/~karkola/topologies.tar

Thanks again,

Sampo


Tsjerk Wassenaar wrote:
> Hi Sampo,
> 
> Thank you for the elaborate account of your problem :)
> 
> So, the problems seem not to be due to grompp, since, when you use the
> old .gro .mdp .top files and run grompp on them, you get the behaviour
> expected from the simulation. Therefore, something happens before. It
> would be very helpful if you could dig a bit deeper. Starting with the
> original pdb files, try to track where the divergent behaviour comes
> from. Are the topologies generated different? Does energy minimization
> in vacuum behave differently between the versions and do these yield
> different results? Etc., etc.
> Besides, does it have to do with your ligand, i.e. do you get the same
> results when you use the protein only?
> 
> Best,
> 
> Tsjerk
> 
> 
> On 3/22/07, Sampo Karkola <sampo.karkola at helsinki.fi> wrote:
>> Dear list,
>>
>> 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.
>> 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):
>>
>> Energy minimisation (hm2 is the new bad behaving simulation and hm5 is
>> the old, good one)
>>
>> 1c1
>> < hm2_em.tpr:
>> ---
>>  > hm5_em.tpr:
>> 78c78
>> <       sc_power             = 0
>> ---
>>  >       sc_power             = 2
>> 89c89
>> <       dihre-fc             = 1000
>> ---
>>  >       dihre-fc             = 1.4013e-42
>> 142c142
>> <       scalefactor          = 1
>> ---
>>  >       scalefactor          = 0
>> 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
>> <             atom[     6]={type=  3, typeB=  3, ptype=    Atom, m=
>> 1.59994e+01, q=-5.56000e-01, mB= 1.59994e+01, qB=-5.56000e-01, resnr=
>>   0} grpnrs=[ 0 0 0 0 0 0 0
>>   0 0 0 ]}
>> ---
>>  >             atom[     6]={type=  2, typeB=  2, ptype=    Atom, m=
>> 1.59994e+01, q=-5.56000e-01, mB= 1.59994e+01, qB=-5.56000e-01, resnr=
>>   0} grpnrs=[ 0 0 0 0 0 0 0
>>   0 0 0 ]}
>>
>> plus a lot of these atom definitions.
>>
>>
>> MD simulation
>>
>> 1c1
>> < hm2_md.tpr:
>> ---
>>  > hm5_md.tpr:
>> 78c78
>> <       sc_power             = 0
>> ---
>>  >       sc_power             = 2
>> 89c89
>> <       dihre-fc             = 1000
>> ---
>>  >       dihre-fc             = 1.4013e-42
>> 143c143
>> <       scalefactor          = 1
>> ---
>>  >       scalefactor          = 0
>> 160,11566c160,11566
>> <       x[    0]={ 2.47200e+00,  2.49800e+00,  2.51500e+00}
>> <       x[    1]={ 2.37100e+00,  2.47900e+00,  2.61100e+00}
>> <       x[    2]={ 2.39700e+00,  2.50800e+00,  2.74600e+00}
>> <       x[    3]={ 2.52300e+00,  2.55600e+00,  2.78600e+00}
>> <       x[    4]={ 2.62400e+00,  2.58300e+00,  2.69000e+00}
>> <       x[    5]={ 2.59800e+00,  2.54700e+00,  2.55500e+00}
>> <       x[    6]={ 2.69600e+00,  2.51500e+00,  2.48800e+00}
>> <       x[    7]={ 2.42800e+00,  2.46600e+00,  2.38500e+00}
>> <       x[    8]={ 2.29600e+00,  2.42000e+00,  2.38200e+00}
>> <       x[    9]={ 2.21300e+00,  2.41600e+00,  2.54400e+00}
>> <       x[   10]={ 2.49800e+00,  2.49100e+00,  2.26500e+00}
>> <       x[   11]={ 2.45600e+00,  2.39700e+00,  2.14900e+00}
>> <       x[   12]={ 2.31700e+00,  2.37400e+00,  2.14600e+00}
>> <       x[   13]={ 2.24100e+00,  2.36700e+00,  2.26400e+00}
>> <       x[   14]={ 2.73500e+00,  2.67900e+00,  2.71500e+00}
>> <       x[   15]={ 2.82900e+00,  2.63400e+00,  2.82800e+00}
>>
>> plus a lot more coordination, velocity, atom type and interaction
>> definitions.
>>
>> 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!
>>
>>
>> Kind regards,
>>
>> Sampo Karkola
>>
>>
>> __________________________________
>>
>> Sampo Karkola
>> Doctoral Student
>>
>> Laboratory of Organic Chemistry
>> Department of Chemistry
>> Faculty of Science
>> PO Box 55 (A.I. Virtasen aukio 1)
>> FIN-00014 University of Helsinki
>> Finland
>>
>> email: sampo.karkola at helsinki.fi
>>
>> tel +358 9 19150369
>> fax +358 9 19150366
>>
>>
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