Hi Justin,<br><br> Thank you so much for your quick reply and good suggestions. The following is my answer.<br><br><div class="gmail_quote">On Wed, May 19, 2010 at 12:50 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;"><div class="im"><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;">
Hi All,<br>
<br>
I understand that the error of segmentation fault may come from many reasons, but I just couldn't figure out the reason of this error in my simulations. I want to run md simulations with explicit water for 20 structures of one domain (residue 77-148) of calmodulin (PDB 1CFC). These 20 starting structures are from one REMD simulation in implicit water. The following is what I did to run simulations for these 20 structures. I used gromacs version 3.1.4 with ffamber ports. The force field is amber03 and water model is TIP3P.<br>
<br>
</blockquote>
<br></div>
Do you have any particular reason for using software that is eight years old? You will get a massive performance upgrade with 4.0.7, as well as the ability to use multiple processors per replica. In versions prior to 4.0, you can only use one processor per REMD replica.<div class="im">
<br></div></blockquote><div>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> </div><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">
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
1. get rid of the steric clash in the starting structure<br>
</blockquote>
<br></div>
What do you mean? Energy minimization? How did you did do this prior to step 2 (generating a topology)?<div class="im"><br></div></blockquote><div>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>
</div><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">
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2. after doing pdb2gmx, then minimze the protein<br>
3, use "-bt dodecahedron -d 0.9 -c" in the command line of editconf<br>
4, after doing genbox, first minimize the water with protein rigid and then minimize the whole system<br>
</blockquote>
<br></div>
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><div class="im"><br></div></blockquote><div>
<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> </div><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">
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
5, run md simulation with position restraint for protein heavy atoms with nose-hoover thermostat for 20ps<br>
6, run NPT simulations with nose-hoover thermostat and 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 some starting structures which could be different in every try. I checked the energy, volume, pressure, temperature, etc for the trajectories which are crashed because of segmentation fault, but nothing was wrong. I roughly checked the trajectory which looks fine. I also couldn't find any useful information from the log file, which looks like the following:<br>
<br>
</blockquote>
<br></div>
Using weak coupling (i.e. Berendsen) coupling is generally recommended for initial equilibration. If a system is far from equilibrium (as it likely will be after adding patterned blocks of water with genbox), the N-H thermostat can allow for wild changes in 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></blockquote><div><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 question. If I choose constraints = hbonds instead of constraints = all-bonds in NPT simulation, what will happen?<br>
<br><br>Best,<br><br>Lan<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
-Justin<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;">
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 appreciated. Thank you.<br>
<br>
<br>
Best,<br>
Lan<br>
<br>
</blockquote>
<br></div></div>
-- <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>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</font></blockquote></div><br>