[gmx-users] Holes in the solvent!

[Arman Mahboubi Soufiani]

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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