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 tr
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 implem
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 hol
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 resul
-users-
> boun...@gromacs.org] On Behalf Of Justin Lemkul
> Sent: Saturday, 27 October 2012 11:25 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Holes in the solvent!
>
>
>
> On 10/26/12 3:25 PM, Arman M. Soufiani wrote:
> > Dear Gromacs users,
On 10/26/12 3:25 PM, Arman M. Soufiani wrote:
Dear Gromacs users,
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
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