[gmx-users] Vacuum simulation in Gromacs 5

[Jan Jirsák]

Ok, thanks -- I see I will have to go back to version 4.5 or 4.6 where
my code worked flawlessly (particle decomposition is available there).

Regarding "flying away" -- sometimes I NEED my system to disintegrate
to fragments which fly away;) Momentum is of course conserved, cause
they fly in opposite directions.

Thank you for the links, I will have a look.
With kind regards
Jan

2015-06-14 19:32 GMT+02:00 V.V.Chaban <vvchaban at gmail.com>:
> There are just two options for such simulations. Either one uses a
> code supporting particle decomposition or adds a vacuum layer.
>
> The fragments will not fly away provided that momentum is conserved.
>
> Some comments on why and what to select may be present here:
>
> http://pubs.acs.org/doi/abs/10.1021/jz500563q
>
> http://pubs.acs.org/doi/abs/10.1021/jz300405q
>
> http://pubs.acs.org/doi/abs/10.1021/jz201190j
>
>
>
>
>
>
> On Sun, Jun 14, 2015 at 2:24 PM, Jan Jirsák <janjirsak at gmail.com> wrote:
>> 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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