Hi Justin,<br><br> I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right?<br><br>Thanks,<br>Lan<br><br><div class="gmail_quote">On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
<br>
Lan Hua wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Hi Justin,<br>
<br>
Thank you so much for your quick reply and good suggestions. The following is my answer.<br>
<br></div><div class="im">
On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Lan Hua wrote:<br>
<br>
Hi All,<br>
<br>
I understand that the error of segmentation fault may come<br>
from many reasons, but I just couldn't figure out the reason of<br>
this error in my simulations. I want to run md simulations with<br>
explicit water for 20 structures of one domain (residue 77-148)<br>
of calmodulin (PDB 1CFC). These 20 starting structures are from<br>
one REMD simulation in implicit water. The following is what I<br>
did to run simulations for these 20 structures. I used gromacs<br>
version 3.1.4 with ffamber ports. The force field is amber03<br>
and water model is TIP3P.<br>
<br>
<br>
Do you have any particular reason for using software that is eight<br>
years old? You will get a massive performance upgrade with 4.0.7, as<br>
well as the ability to use multiple processors per replica. In<br>
versions prior to 4.0, you can only use one processor per REMD replica.<br>
<br>
The reason that I am using gromacs 3.1.4 is to prepare some input files for simulations at folding@home in which version 3.1.4 is recommended.<br>
<br>
</div></blockquote>
<br>
OK, as long as you've got a reason...<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
1. get rid of the steric clash in the starting structure<br>
<br>
<br>
What do you mean? Energy minimization? How did you did do this<br>
prior to step 2 (generating a topology)?<br>
<br>
I used the "protein preparation wizard" which is implemented in maestro package to do this. Actually in this wizard, energy minimization is performed on protein.<br>
<br>
<br>
2. after doing pdb2gmx, then minimze the protein<br>
3, use "-bt dodecahedron -d 0.9 -c" in the command line of<br>
editconf<br>
4, after doing genbox, first minimize the water with protein<br>
rigid and then minimize the whole system<br>
<br>
<br>
A lot of these steps are redundant and probably unnecessary. Some tips:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br>
<br>
<br>
Thanks for the tips. I went to the link, but I am still a little bit confused about which steps are unnecessary. You mean step 7 and step 8? I did this in case simulations at F@H would be crashed.<br>
<br>
</blockquote>
<br></div>
I just mean the repeated, separate energy minimizations. I guess there's no harm in it, but generally I find that minimizing the protein in vacuo, then with and without restraints in solvent, etc. is unnecessary. I'd suggest just building the system (solvent and all), and minimizing the whole thing (without restraints). I don't think you stand to gain anything with your procedure.<div>
<div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
5, run md simulation with position restraint for protein<br>
heavy atoms with nose-hoover thermostat for 20ps<br>
6, run NPT simulations with nose-hoover thermostat and<br>
Parrinello-Rahman thermostat for 500ps<br>
7, run NVT simulation for another 100ps<br>
8, then energy minimze the whole system again.<br>
<br>
Every time, there are always "segmentation fault" in step 6 for<br>
some starting structures which could be different in every try.<br>
I checked the energy, volume, pressure, temperature, etc for<br>
the trajectories which are crashed because of segmentation<br>
fault, but nothing was wrong. I roughly checked the trajectory<br>
which looks fine. I also couldn't find any useful information<br>
from the log file, which looks like the following:<br>
<br>
<br>
Using weak coupling (i.e. Berendsen) coupling is generally<br>
recommended for initial equilibration. If a system is far from<br>
equilibrium (as it likely will be after adding patterned blocks of<br>
water with genbox), the N-H thermostat can allow for wild changes in<br>
the temperature of the system, leading to a collapse.<br>
<br>
Your temperature coupling groups are also inappropriate:<br>
<br>
Tcoupl = nose-hoover<br>
tc_grps = Protein SOL Na<br>
tau_t = 0.1 0.1 0.1<br>
<br>
Never couple solvent and ions separately; it can lead to instability:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Thermostats" target="_blank">http://www.gromacs.org/Documentation/Terminology/Thermostats</a><br>
<br>
<br>
These are good suggestions. Thanks. So use Berendsen coupling for both temperature and pressure coupling for initial equilibration, for example position restrained NVT followed by NPT, right? I have another <br>
</blockquote>
<br></div></div>
At least for the thermostat, but yes, probably it can't hurt to use weak coupling for both temperature and pressure.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
question. If I choose constraints = hbonds instead of constraints = all-bonds in NPT simulation, what will happen?<br>
<br>
</blockquote>
<br></div>
You constrain heavy atom-H bonds instead of all bonds. Using fewer constraints may or may not affect the magnitude of the time step you can use, but generally X-H bonds are the highest frequency and thus are the least stable with long time steps.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
Best,<br>
<br>
Lan<br>
<br>
<br>
-Justin<br>
<br>
<br>
Step Time Lambda Annealing<br>
180000 360.00003 0.00000 1.00000<br>
<br>
Rel. Constraint Deviation: Max between atoms RMS<br>
Before LINCS 0.045887 47 48 0.004584<br>
After LINCS 0.000020 752 755 0.000003<br>
<br>
Energies (kJ/mol)<br>
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14<br>
2.08335e+03 1.59908e+02 2.95659e+03 1.17109e+03 1.27711e+04<br>
LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential<br>
4.10779e+04 -1.37728e+03 -2.89916e+05 -5.82443e+04 -2.89318e+05<br>
Kinetic En. Total Energy Temperature Pressure (bar)<br>
5.25584e+04 -2.36759e+05 2.96920e+02 -1.07683e+02<br>
<br>
Step Time Lambda Annealing<br>
185000 370.00003 0.00000 1.00000<br>
<br>
Rel. Constraint Deviation: Max between atoms RMS<br>
Before LINCS 0.052014 70 71 0.005149<br>
After LINCS 0.000011 214 215 0.000002<br>
<br>
Energies (kJ/mol)<br>
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14<br>
2.33684e+03 1.42695e+02 2.91169e+03 1.18452e+03 1.28507e+04<br>
LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential<br>
4.06987e+04 -1.37332e+03 -2.88889e+05 -5.83180e+04 -2.88455e+05<br>
Kinetic En. Total Energy Temperature<br>
<br>
The *.mdp files are also attached. Any help will be highly<br>
appreciated. Thank you.<br>
<br>
<br>
Best,<br>
Lan<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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