[gmx-users] GROMACS 4.5.4 keep crashing all the time.

[Matthew Zwier]

My apologies; the remainder of the thread in which these suggestions
were already proposed and discussed showed up where I didn't expect
them.  Sorry to repeat what's already been said.

MZ

On Thu, Aug 18, 2011 at 12:58 PM, Matthew Zwier <mczwier at gmail.com> wrote:
> Hi Itamar,
>
> In my experience, the 4.5 series appears to be slightly less tolerant
> of unstable systems than the 4.0 series.  Try minimizing and/or
> equilibrating your system longer.  See
> http://www.gromacs.org/Documentation/Errors and
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> MZ
>
>
> On Wed, Aug 17, 2011 at 7:16 PM, Itamar Kass (Med)
> <itamar.kass at monash.edu> wrote:
>> Hi Matthew,
>>
>> Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I
>> used both GROMACS compiled by me (on my machine) or by the sys-admin on
>> Linux cluster or blue-gene.
>>
>> The simulations using 4.5.4 crashed giving LINCS error, which is not the
>> case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks
>> it is poorly compiled bin, as I used both GROMACS compiled with me (on my
>> machine) or by the sys-admin on Linux cluster/blue-gene.
>>
>> cheers,
>> Itamar
>