[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

[Tsjerk Wassenaar]

Hi Simone,

The temperature coupling might be a cause for an error like that to
occur. Try to understand that coupling ions separately may cause large
fluctuations in there velocities and hence cause sudden large
displacements that may put an ion on top of a solvent molecule that
can't be settled anymore due to that.

I assume you fixed that error, but think it's good to have a bit of
background (and please read some more) to help avoiding such mistakes
later on. If the problem persists while the T-coupling error is fixed,
then there's something else wrong :) Is it always the same water
molecule, or are they always in the neighbourhood, or does the error
occur at random water molecules? Is the water molecule close to the
edge of the box when the error occurs? Since you have all frames, you
can easily check the trajectory all the way :) You may also try
running with NVT to see whether that fixes the problem. Did you
actually equilibrate the temperature first, before putting the
pressure on? O, and you might want to show your md.mdp, as that's
where the simulation is breaking.

Hope it helps,

Tsjerk

On Fri, Oct 16, 2009 at 1:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Simone Cirri wrote:
>>
>> Justin A. Lemkul wrote:
>>
>>    ; Berendsen temperature coupling is on in three groups
>>    Tcoupl              =  berendsen
>>
>>    tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+
>>
>>    ref_t               =  300      300     300
>>
>>    Never couple solvent and ions separately. Surely grompp warned you
>>    that you should be using "Protein Non-Protein"? See here:
>>
>>    http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>>
>> Hi Justin, thanks for the suggestion. Actually, it's an error I've always
>> been doing and I'm glad I've solved it.
>> However, I'm afraid it has nothing to do with the problem, because I just
>> tried to run the MD again (after modifying the md.mdp as you told me) and
>> the fatal error is still there.
>> I've noticed the the T-coupling mistake is also in pr.mdp. Do you think
>> that correcting it and re-running the PR simulation would fix the "water
>> molecule can not be settled" problem?
>
> It's probably worth a shot.  It's not appropriate to couple solvent and ions
> separately in any phase, equilibration or data collection.
>
> -Justin
>
>> Anyway here is the pr.mdp (as it was before):
>>
>> title               =  hsacyx
>> warnings            =  10
>> cpp                 =  /lib/cpp
>> define              =  -DPOSRES
>> constraints         =  all-bonds
>> integrator          =  md
>> dt                  =  0.002    ; ps !
>> nsteps              =  100000    ; total 200.0 ps.
>> nstcomm             =  1
>> nstxout             =  250
>> nstvout             =  1000
>> nstfout             =  0
>> nstlog              =  10
>> nstenergy           =  10
>> nstlist             =  10
>> ns_type             =  grid
>> rlist               =  0.9
>> coulombtype        =  PME
>> rcoulomb            =  0.9
>> rvdw                =  0.9
>> fourierspacing        =  0.12
>> fourier_nx        =  0
>> fourier_ny        =  0
>> fourier_nz        =  0
>> pme_order        =  6
>> ewald_rtol        =  1e-5
>> optimize_fft        =  yes
>> ; Berendsen temperature coupling is on in four  groups
>> Tcoupl              =  berendsen
>> tau_t               =  0.1     0.1    0.1
>> tc-grps            =  Protein     SOL    NA+
>> ref_t               =  300     300    300
>> ; Pressure coupling is on
>> Pcoupl              =  berendsen
>> pcoupltype          =  isotropic
>> tau_p               =  0.5
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel             =  yes
>> gen_temp            =  300.0
>> gen_seed            =  173529
>>
>> Thank you
>>
>> Simone Cirri
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623