[gmx-users] Holes in the solvent!

[Richard Broadbent]

Dear Arman,

I have never seen holes appear in my solvent when running on 12 cores or 
fewer, or when running with langevin coupling or NVE.

Running at higher temperatures (700K-1000K) did remove the holes from my 
system however, the RDF's were inconsistent on varying core counts 
(peeks and troughs moving by Angstroms). Low core counts tended to yeild 
the same RDF as a well thermalised and equilibrated NVE run or a 
langevin simulation.


I currently have simulations queing which will use v-rescale so I can't 
comment on that thermostat yet but if you are seeing this on 1 core I 
don't think it is the same issue I've been seeing.

Sorry,

Richard



On 30/10/12 08:56, Arman Mahboubi Soufiani wrote:
> Dear Richard,
>
> Thank you for your kind response. I'm glad that my problem is not a rare
> one. Actually, I apply the simplest V-rescale as the thermostat. I run my
> system on one core! However, I have not tried turning off the thermostat
> and run a micro-canonical instead.
> Well, I got an idea to implement. I am going to try NPTs at high
> temperatures and anneal the system in order to find out whether I can get
> rid of these large voids (holes) or not! Do you have any idea if this can
> work or not?!
>
> Looking forward to hearing from you.
>
> Best Wishes
>
> Arman
>
> On Tue, Oct 30, 2012 at 8:35 AM, Broadbent, Richard <
> richard.broadbent09 at imperial.ac.uk> wrote:
>
>> Dear Arman,
>>
>> I've noticed a similar effect where large voids appear in a solvent when
>> running long nose-hoover NVT simulations. I have checked and it is not a
>> pbc
>> artefact.
>> I found that if I turn the thermostat off the holes go away. I've also
>> found
>> that reducing the number of cores removes the holes. I am currently
>> investigating this for a bug report I submitted (
>> http://redmine.gromacs.org/issues/1012 )
>>
>> It would be helpful if you could let me know if your using a nose-hoover
>> thermostat and if so have a look at what happens if you run the system on
>> fewer cores, and what happens if you turn off the thermostat (and run nve)
>> after the system has equilibrated.
>>
>> Thanks,
>>
>> Richard
>>
>>
>>
>> On 30/10/2012 05:46, "Arman Mahboubi Soufiani" <armansoufiani at gmail.com>
>> wrote:
>>
>>> Dear Chris,
>>>
>>> Thank you for your directions. NaCl concentration in my system is 0.14 M
>>> and I often visualize the whole system and can see the ions around the
>>> system but not in crystal form!
>>> Well, it sounds really strange to me! And I don't know if I proceed with
>>> such a system, I get scientific results or not?!
>>> I appreciate your further helps.
>>>
>>> Best Regards
>>>
>>> Arman
>>>
>>> On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale <
>>> chris.neale at mail.utoronto.ca> wrote:
>>>
>>>> In addition to the comments of Dallas Warren, which seems quite possible
>>>> and should be checked,
>>>> are you sure that you are seeing real holes and not just salt crystals
>>>> that look like holes when you render only
>>>> the waters with VMD? I have found that, at NaCL concentrations above 1
>> M,
>>>> lipid bilayers catalyze the formation
>>>> of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field
>>>> for ions. These crystals looked a lot
>>>> like vacuum holes to me until I visualized the salt.
>>>>
>>>> Chris.
>>>>
>>>> -- original message --
>>>>
>>>> I am simulating a protein on a polymer surface for further adsorption
>> free
>>>> energy calculation.
>>>> However, after performing the NVT run either for short or long
>> durations I
>>>> found out that couple of holes appear in the physiological saline
>> solution
>>>> (solvent)!!!
>>>> Additionally, even proceeding with a long NPT run the holes are still
>>>> present in the system.
>>>> I would be thankful if you could direct me what could be source of such
>> a
>>>> strange outcome.
>>>>
>>>> Best Wishes
>>>>
>>>> Arman
>>>>
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