[gmx-users] Implicit solvent crashes with PD

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 12 06:42:04 CEST 2011

Mark Abraham wrote:
> On 12/07/2011 4:51 AM, Justin A. Lemkul wrote:
>> Hi All,
>> I'm having a strange problem with some implicit solvent systems and 
>> I'm wondering if anyone's experienced the same problem or if I've 
>> stumbled upon a bug.  I'm testing some methodology with a robust 
>> system (everyone's favorite, 1AKI lysozyme).  Running simulations with 
>> finite cutoffs works fine (in serial or parallel using DD), but if I 
>> try to call the all-vs-all kernels (e.g. infinite cutoffs), the 
>> simulations instantly crash (at step 0) with LINCS warnings.  Running 
>> in serial, however, produces perfectly stable trajectories using 
>> all-vs-all, but the simulations are very slow.
>> The effects are independent of integrator (tested sd and md) and 
>> hardware/compilers.  The problem is reproducible on two very different 
>> systems:
>> 1. x86_64 via OpenMPI 1.4.2 and compiled with cmake with gcc-4.3.4
>> 2. Mac OSX with threads and compiled via autoconf with gcc-4.4.4
>> All force fields that I've tested (OPLS-AA, CHARMM27, and AMBER03) 
>> give the same result.
>> The problem is present in version 4.5.4 and the most current 
>> release-4-5-patches.  My .mdp file and a gdb backtrace are provided at 
>> the end of this message.
>> Is there anything else to try, or should I just file a redmine issue 
>> with a .tpr file?
> Judging by the .mdp file, I have similar systems working just fine in 
> parallel. If you upload the .tpr to Redmine, I'll try it out.

Thanks Mark.  I've created issue #777 for this.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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