<div>Hi Sampo, </div>
<div> </div>
<div>I don't know if this is obvious to you but when you start a simulation from a energy-minimized configuration you should use</div>
<div> </div>
<div><em>grompp -t minimization.trr -c minimization_out.gro</em> (here you will use a full-precision configuration)</div>
<div> </div>
<div>and not only</div>
<div> </div>
<div><em>grompp -c minimization_out.gro</em> (in contrast, here you will have a configuration with rounding errors)<br> </div>
<div>It seems that your system is far from trivial and has to be very well energy-minimized before starting an MD run.</div>
<div> </div>
<div>Regards,</div>
<div> </div>
<div>Pedro. <br> </div>
<div><span class="gmail_quote">2007/3/22, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Sampo Karkola wrote:<br>> Dear list,<br><br>Thanks for the good problem description!<br><br>> I am trying to simulate a crystal structure of a protein with a cofactor
<br>> (NADP, I've used NDPP topology) and a (self-made) ligand in a box of<br>> water. The preparation of the simulation went normally: pdb2gmx,<br>> editconf, genbox, grompp (for ions), genion, grompp (for em) mdrun (em),
<br>> grompp (for md), mdrun (md). Now, in the md simulation, the potential<br>> and total energies of the system rise immediately from the beginning,<br>> stabilize to a certain level and later the run crashed with LINCS
<br>> warnings. Earlier I have succesfully simulated a model of an another<br>> enzyme with similar procedure and in that run the potential energy<br>> decreased immediately and stabilized with no crashes. I tried to
<br>> simulate the protein alone, the cofactor alone and the ligand alone and<br>> the energies rise in all cases.<br>><br>> Luckily, I had an older simulation (with gromacs 3.2.1, now I'm using<br>> 3.3.1
) with the same ligand (except one atom type is changed from NR in<br>> the old topology to N in new topology) alone and there the energies<br>> decreased as they should. To study the differences in the ligand-alone
<br>> simulations, I performed an mdrun with the old tpr file (mdrun -s<br>> old.tpr -o new_run -c new_run...) and the energies decreased again, as<br>> they should. Next, I grompped a new tpr-file from the old gro, top and
<br>> mdp files, got a new tpr file and simulated it resulting in decreasing<br>> energies again. But when I try to do the whole process from the<br>> beginning using the same pdb file as in the older run something goes
<br>> differently and the mdrun produces rising energies. The energy<br>> minimisation with the new run takes over 3000 steps while the old run<br>> was minimised in 34 steps. I've checked that the gro and top files
<br>> between the old (working) and the new (non-working) runs are identical.<br><br>So far everything looks good to me.<br><br>> The only differences I find are in the tpr files of the energy<br>> minimisation and md simulation and they look like this (compared with
<br>> diff):<br><br>gmxcheck -s1 old.tpr -s2 new.tpr is the recommended way to check for<br>this sort of thing.<br><br>> 22983c22983<br>> < atom[ 4]={type= 2, typeB= 2, ptype= Atom, m=<br>
> 1.40067e+01, q= 4.80000e-02, mB= 1.40067e+01, qB= 4.80000e-02, resnr=<br>> 0} grpnrs=[ 0 0 0 0 0 0 0<br>> 0 0 0 ]}<br>> ---<br>> > atom[ 4]={type= 1, typeB= 1, ptype= Atom, m=<br>
> 1.40067e+01, q= 4.80000e-02, mB= 1.40067e+01, qB= 4.80000e-02, resnr=<br>> 0} grpnrs=[ 0 0 0 0 0 0 0<br>> 0 0 0 ]}<br>> 22985c22985<br>> plus a lot of these atom definitions.<br><br>These seem strange to me - the "type" values in the above arrays should
<br>be indices into an atomtype array earlier in the .tpr file, but if the<br>above values are right, and the two atoms 4 should correspond, then the<br>atomtype array should also be different... but diff is not reporting
<br>this, and I do not understand why. Does gmxcheck differ? (Recall that<br>this is not the fourth atom, since numbering starts at zero).<br><br>> plus a lot more coordination, velocity, atom type and interaction<br>> definitions.
<br><br>Evidently, since the starting configuration is embedded in the .tpr and<br>the endpoint of the previous minimization was different.<br><br>> I have no dihedral restraints applied and those sc_power, dihre-fc and
<br>> scalepower definitions are different even in the old, working simulation<br>> and in the one which was grompped again and producing correct results<br>> with decreasing energies.<br>><br>> So the problem is that the old gro, top and mdp files give correct
<br>> results even with grompped again, but a new procedure starting from the<br>> pdb file give bad results.<br>><br>> I was hoping that someone could direct me to the correct direction and<br>> find out what's wrong. All suggestions are highly appreciated and tested!
<br><br>Not much joy from me, I'm afraid!<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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