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)
________________________________ 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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
