[gmx-users] confusion about segmentation fault during mdrun
Lan Hua
lan.hua at gmail.com
Thu May 20 03:08:19 CEST 2010
Thanks. The simulations are regular MD in explicit water at room
temperature.
Lan
On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Lan Hua wrote:
>
>> Hi Justin,
>>
>> I appreciated your quick answers. So if I understand correctly, using
>> constraints = hbonds with the time step of 2fs, it should be fine, right?
>>
>>
> Maybe. If your goal is REMD (I'm not clear from your original post) then
> stability may be an issue at higher temperatures, in which case you may need
> to constrain all bonds or decrease your time step, maybe both. At ambient
> temperatures, what you propose is likely stable. Look into the relevant
> literature for similar force fields and applications to be sure.
>
> -Justin
>
> Thanks,
>> Lan
>>
>>
>> On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Lan Hua wrote:
>>
>> Hi Justin,
>>
>> Thank you so much for your quick reply and good suggestions.
>> The following is my answer.
>>
>> On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>> Lan Hua wrote:
>>
>> Hi All,
>>
>> 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.
>>
>>
>> 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.
>>
>> The reason that I am using gromacs 3.1.4 is to prepare some
>> input files for simulations at folding at home in which version
>> 3.1.4 is recommended.
>>
>>
>> OK, as long as you've got a reason...
>>
>>
>>
>>
>> 1. get rid of the steric clash in the starting structure
>>
>>
>> What do you mean? Energy minimization? How did you did do this
>> prior to step 2 (generating a topology)?
>>
>> 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.
>>
>> 2. after doing pdb2gmx, then minimze the protein
>> 3, use "-bt dodecahedron -d 0.9 -c" in the command
>> line of
>> editconf
>> 4, after doing genbox, first minimize the water with
>> protein
>> rigid and then minimize the whole system
>>
>>
>> A lot of these steps are redundant and probably unnecessary.
>> Some tips:
>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>
>>
>> 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 at H would be
>> crashed.
>>
>>
>> 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.
>>
>>
>>
>>
>> 5, run md simulation with position restraint for protein
>> heavy atoms with nose-hoover thermostat for 20ps
>> 6, run NPT simulations with nose-hoover thermostat and
>> Parrinello-Rahman thermostat for 500ps
>> 7, run NVT simulation for another 100ps
>> 8, then energy minimze the whole system again.
>>
>> 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:
>>
>>
>> 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.
>>
>> Your temperature coupling groups are also inappropriate:
>>
>> Tcoupl = nose-hoover
>> tc_grps = Protein SOL Na
>> tau_t = 0.1 0.1 0.1
>>
>> Never couple solvent and ions separately; it can lead to
>> instability:
>>
>> http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>>
>> 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
>>
>>
>> At least for the thermostat, but yes, probably it can't hurt to use
>> weak coupling for both temperature and pressure.
>>
>>
>> question. If I choose constraints = hbonds instead of
>> constraints = all-bonds in NPT simulation, what will happen?
>>
>>
>> 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.
>>
>> -Justin
>>
>>
>> Best,
>>
>> Lan
>>
>> -Justin
>>
>>
>> Step Time Lambda Annealing
>> 180000 360.00003 0.00000 1.00000
>>
>> Rel. Constraint Deviation: Max between atoms RMS
>> Before LINCS 0.045887 47 48 0.004584
>> After LINCS 0.000020 752 755 0.000003
>>
>> Energies (kJ/mol)
>> Angle Proper Dih. Ryckaert-Bell.
>> LJ-14 Coulomb-14
>> 2.08335e+03 1.59908e+02 2.95659e+03
>> 1.17109e+03 1.27711e+04
>> LJ (SR) Disper. corr. Coulomb (SR) Coulomb
>> (LR) Potential
>> 4.10779e+04 -1.37728e+03 -2.89916e+05
>> -5.82443e+04 -2.89318e+05
>> Kinetic En. Total Energy Temperature Pressure (bar)
>> 5.25584e+04 -2.36759e+05 2.96920e+02 -1.07683e+02
>>
>> Step Time Lambda Annealing
>> 185000 370.00003 0.00000 1.00000
>>
>> Rel. Constraint Deviation: Max between atoms RMS
>> Before LINCS 0.052014 70 71 0.005149
>> After LINCS 0.000011 214 215 0.000002
>>
>> Energies (kJ/mol)
>> Angle Proper Dih. Ryckaert-Bell.
>> LJ-14 Coulomb-14
>> 2.33684e+03 1.42695e+02 2.91169e+03
>> 1.18452e+03 1.28507e+04
>> LJ (SR) Disper. corr. Coulomb (SR) Coulomb
>> (LR) Potential
>> 4.06987e+04 -1.37332e+03 -2.88889e+05
>> -5.83180e+04 -2.88455e+05
>> Kinetic En. Total Energy Temperature
>>
>> The *.mdp files are also attached. Any help will be highly
>> appreciated. Thank you.
>>
>>
>> Best,
>> Lan
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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