[gmx-users] Stuck --> unstuck ...

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 14 11:18:43 CEST 2007

Stéphane Téletchéa wrote:
> David van der Spoel a écrit :
>> Stéphane Téletchéa wrote:
>>> I've found out where the problem lie (at least one of ...).
>>> Small reminder: i've tried to setup a system consisting of HIV 
>>> protease + one ligand on a water box. I used the excellent protocol 
>>> from John E. Kerrigan (Drug-enzyme tutorial) in order to set up my 
>>> simulation and encountered some problems with it (basically: Box was 
>>> shifted at least 10 times. Please see log-file.).
>>> I add some constructive comments on ways to explore where the problem 
>>> was (changing the protocol, including ions into the water to get a 
>>> better coupling bath, etc.). Thanks to all of them, even if sometimes 
>>> humour is hard to catch by email!
>>> I'm not interested in the system per se (i've done other dynamics 
>>> working fine with this protocol) but was rather interested in 
>>> providing an updated way of doing a drug-enzyme tutorial with latest 
>>> force fields (g45a3, g53a6) and using the latest prodrg (since it 
>>> allow the output of  g43a1-type atoms, mostly transferable to the 
>>> newer ones).
>>> I'll put this on the wiki soon.
>>> I've checked many parameters except one: all-bons vs hbonds.
>>> I do not recall a 'rationale' reason for using the all-bonds 
>>> parameter (instead of hbonds where it worked for other dynamics 
>>> simulations) but the fact is that if i run all-bonds simulations 
>>> (whatever the starting system) with NVT+NPT, i see a crash with the 
>>> error message like this:
>>> Step 1  Warning: pressure scaling more than 1%, mu: -1.59647e+20 
>>> -1.59647e+20 -1.59647e+20
>>> Correcting invalid box:
>>> old box (3x3):
>>>    old box[    0]={-9.82630e+20,  0.00000e+00, -0.00000e+00}
>>>    old box[    1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
>>>    old box[    2]={ 0.00000e+00,  0.00000e+00, -1.12456e+21}
>>> new box (3x3):
>>>    new box[    0]={-9.82630e+20,  0.00000e+00, -0.00000e+00}
>>>    new box[    1]={ 0.00000e+00, -8.90833e+20, -0.00000e+00}
>>>    new box[    2]={ 0.00000e+00,  8.90833e+20, -1.12456e+21}
>>> using the *same* protocol (same starting structures, etc) and only 
>>> changing all-bonds to h-bonds leads to a 'normal' trajectory (no 
>>> error, no warning, no crash).
>>> I remember gromacs 3.3.0 had a problem where pme=4 (that lead to the 
>>> 3.3.1 rapid release). There are a lot of reports on this mailing-list 
>>> with crash/segfaults when using all-bonds, and it seems more when 
>>> all-bonds are used instead of h-bonds.
>>> Of course it may come from not completely converged dynamics (my 
>>> setup is very rapid, the 4 PR steps last only 100 ps), from not 
>>> enough minimsed structures, etc.
>>> Could it be also possible there is a problem while using all-bonds 
>>> (even with a 2fs time step) instead of in gromacs, and pme_order was 
>>> just hiding it ?
>> I don't think so. All-bonds with 2 fs should work reliably with both 
>> lincs and shake, provided your system is equilibrated to some extent.
> I'm ready to provide again detailed steps i've followed, but on 
> different systems, including systems coming from a working gromacs run 
> (for instance a snapshot after 10 ns of production) the problem arises 
> when i switch from h-bonds to all-bonds.
> There are many reports about segfaults in gromacs while using all-bonds 
> constraints, this was assumed to be related to pme (and gromacs 3.3.1 
> was released to correct this). I *suppose* this may hide another problem 
> and pme is not alone the culprit.
> I'll try to continue this on bugzilla with input files, procedure on the 
> wiki (since the procedure in itself works with h-bonds) so we can 
> decipher where this comes from..
> Cheers,
> Stéphane
Please do. I've just fixed a problem with constraints=h-bonds (where 
molecules are split over processors). See bugzilla 109.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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