[gmx-users] Vacuum simulation in Gromacs 5

[V.V.Chaban]

Why don't you simply surround your molecule with a layer of vacuum and
use all periodic set of details as normally? This is what people do in
the plane-wave codes when the so-called 'cluster representation' is
desired.




On Sun, Jun 14, 2015 at 1:54 PM, Jan Jirsák <janjirsak at gmail.com> wrote:
> Hi,
>
> I did the test and found out that -nt 8 is even slower than -nt 1 !!
> However, I think that simulation hasn't even properly started with 8
> threads and got stuck somewhere in the beginning.
>
> Details:
> I used a short run (1000 steps) for testing. mdrun -nt 1 finished
> after ca 11 hours, whereas not a single checkpoint or run log record
> have been saved for mdrun -nt 8 (and simulation is still running). Not
> even starting energies were displayed - last record in a log file is a
> SETTLE citation.
>
> In top I noticed both processes used up to 100% CPU, but considerably
> differed in the use of memory. Relevant lines:
> PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
> 117710 jan       20   0 5313776 4.642g   9940 R  98.9  3.7  52:47.19
> mdrun
> 117686 jan       20   0  547344  24456   8712 R  92.7  0.0  54:48.92 mdrun
>
> The first listed process (117710) is the single thread simulation (-nt 1).
>
> Thank you for any insight,
> Jan
>
> 2015-06-12 14:35 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>> Hi,
>>
>> Top need not be indicative. Run the same with -nt 1 and observe whether the
>> performance changes. And don't run anything else on these cores.
>>
>> Mark
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