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Hi to all developers,<br>
<br>
We have been using GMX here in the group for almost a decade and we
are familiar with almost all versions of the package.<br>
Recently, when testing the newer versions (4.5.x) using Reaction
Field in a simple lysozyme system (4LZT), my system crashed
constantly.<br>
<br>
System: 4LZT (129 a.a.) directly from PDB databank.<br>
Water: ~6250 molecules<br>
GMX: 4.5.x (all versions tested)<br>
ForceField: Gromos 53A6<br>
Long range elect.: RF, RF-nec, GRF or simply "Cutoff" (all with same
fate.. crash!)<br>
Ensemble: NPT or NVT<br>
<br>
So, what do we already know about the problem:<br>
- The crash always starts in the NH bond present in the amides
(main chain or side chains of GLN and ASN). In the stepxxxx.pdb, we
observe the hydrogen jumping out of place.<br>
- The stability of the simulation is dependent on the quality of
the minimization/initialization procedure. Simple/regular procedures
leads to crashs within 10 ns of simulation. More elaborate protocols
of minimization/initialization can delay the crashs a little longer.<br>
- The system crashes independently of the number of "threads" used
(1-12).<br>
- The instability only leads to crashs when dealing with proteins
>100 a.a.. Simulating a 15 a.a. peptide for over 1 microsecond
does not lead to a crash.<br>
- No problem/crash is observed when using PME.<br>
- No problem/crash is observed when using GMX versions prior to
4.0.7.<br>
<br>
My question is this, what might have happen with the RF code between
versions 4.0.x and 4.5.x that leads to this problem? Or is there any
specific parameter to be used with RF/Cutoff to avoid these
problems?<br>
<br>
Even though RF is not very popular with GMX developers, it has been
essential for the development of our in house Constant-pH MD method
(<a
href="http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation?highlight=constant+pH">http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation</a>).<br>
<br>
On a typical MD run we use the following MDP file, or a similar one.<br>
<br>
________________<br>
integrator = md<br>
tinit = 0<br>
dt = 0.002<br>
nsteps = 5000000<br>
comm-mode = Linear<br>
nstcomm = 1<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 5000<br>
nstenergy = 5000<br>
nstxtcout = 5000<br>
xtc-precision = 1000<br>
energygrps = Protein SOL<br>
nstlist = 5<br>
ns_type = grid<br>
pbc = xyz<br>
periodic_molecules = no<br>
rlist = 0.9<br>
coulombtype = Reaction-Field<br>
rcoulomb-switch = 0<br>
rcoulomb = 1.4<br>
epsilon_r = 1<br>
epsilon_rf = 54<br>
vdwtype = Cut-off<br>
rvdw-switch = 0<br>
rvdw = 1.4<br>
DispCorr = No<br>
tcoupl = berendsen<br>
tc-grps = Protein SOL<br>
tau-t = 0.1 0.1<br>
ref-t = 298.15 298.15<br>
Pcoupl = berendsen<br>
Pcoupltype = Isotropic<br>
tau-p = 0.5<br>
compressibility = 4.5e-5<br>
ref-p = 1<br>
refcoord_scaling = No<br>
gen_vel = no<br>
constraints = all-bonds<br>
constraint_algorithm = lincs<br>
lincs-order = 4<br>
lincs-iter = 1<br>
lincs-warnangle = 90<br>
___________________________<br>
<br>
Thank you for any help you can assist us.<br>
<br>
Regards,<br>
Miguel<br>
<br>
<pre class="moz-signature" cols="72">--
============================================
Miguel Machuqueiro
Department of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
Campo Grande, Edifício C8 (sala 8.5.47)
1749-016 Lisboa, Portugal
Tel. : +351 217500112 (int.ext.28547)
Mobile: +351 967562285
E-mail: machuque at fc.ul.pt
www1: <a class="moz-txt-link-freetext" href="http://webpages.fc.ul.pt/~mamachuqueiro">http://webpages.fc.ul.pt/~mamachuqueiro</a>
www2: <a class="moz-txt-link-freetext" href="http://intheochem.fc.ul.pt">http://intheochem.fc.ul.pt</a>
______________________________________________
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