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 <jalem...@vt.edu>
*To:* Bahar Mehrpuyan <baharmehrpu...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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
========================================
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