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

[David van der Spoel]

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.
________________________________________________________________________
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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