[gmx-users] Vacuum simulation in Gromacs 5

V.V.Chaban vvchaban at gmail.com
Sun Jun 14 19:33:15 CEST 2015


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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