[gmx-users] npt equilbration + density

[Justin Lemkul]

On 2/8/13 11:54 AM, Bahar Mehrpuyan wrote:
> Thanks Justin for the reply.
>   i use SPC water model (12000 molecules). in literature there are different
> values for density which depend simulation time, number of water molecules ,
> etc. (for example this paper : jcp.aip.org/resource/1/jcpsa6/v108/i24/p10220_s1)
>

The results will also depend to a much larger extent on the proper use of 
cutoffs, long-range electrostatics algorithms, etc.  People get different 
results when making changes.  Somewhere in the ballpark of 980 kg m^-3 seems 
about right for SPC, but a proper assessment would require comparison with work 
that uses the same run parameters that you did.

-Justin

> --------------------------------------------------------------------------------
> *From:* Justin Lemkul <jalemkul at vt.edu>
> *To:* Bahar Mehrpuyan <baharmehrpuyan at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> *Sent:* Friday, February 8, 2013 7:56 PM
> *Subject:* Re: [gmx-users] npt equilbration + density
>
>
>
> On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote:
>  > Dear gmx users
>  >
>  >
>  > My system is a single amino acid in water. I use two stage equilibration :
> NVT (300 k) and NPT (300k , 1 barr) with position restrain.
>  >
>  > NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure.
>  >
>  > but density is 974.031 . is this reasonable?
>  >
>
> That depends on the water model you use and what its expected density is.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================