[gmx-users] Vacuum simulation in Gromacs 5

[Jan Jirsák]

Thank you for a reply - I could try that when everything else fails, but
(i) my system can disintegrate and its fragments can fly really long
distances apart, so the layer of vacuum would have to be considerably
(and unpredictably) thick - the same applies to cutoffs,
(ii) in principle I don't see why one should bother with periodic
images in a simulation which is inherently non-periodic.
Regards, Jan


2015-06-14 19:01 GMT+02:00 V.V.Chaban <vvchaban at gmail.com>:
> 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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