[gmx-users] radius of gyration

[delara aghaie]

Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to calculate it via MD simulation for calcium pump protein. Following the same method as described in justin lezozyme tutorial, we have dissolved the protein in water.
I want to know that is it wise to study this parameter for this protein out of membrane and only in the box of water???
Thanks
regards
D.M



________________________________
 From: Anja Kuhnhold <anja.kuhnhold at physik.uni-halle.de>
To: gmx-users at gromacs.org 
Sent: Friday, 8 June 2012, 12:29
Subject: [gmx-users] Re: energy conservation: shift vs shifted user potential
 
Hello all,

can someone give me a hint, please?
Do you need more information?
Has anyone had a similar problem.

I really need to figure that out, because I will simulate other systems
which can be run only with user tables.

Anja



-
> ----- Original Message -----
> ----- Original Message -----
> From Anja Kuhnhold <anja.kuhnhold at physik.uni-halle.de>
> Date Wed, 06 Jun 2012 15:07:40 +0200
> To gmx-users at gromacs.org
> Subject [gmx-users] energy conservation: shift vs shifted user potential
> Dear gmx-users,
> 
> I have a problem concerning energy conservation when using user 
> potentials (tables).
> I'm using gromacs 4.5.4
> I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 
> chains a 10 beads in a 26x26x26 periodic box).
> 
> I tried different vdwtypes (cutoff always 3.24):
> The cut-off version does not conserve energy -- okay.
> The shift and switch versions conserve energy -- fine.
> 
> Now I wanted to do the same with user tables:
> Simple Lennard-Jones table gives really the same results as the 
> cut-off version -- good.
> 
> But if I use a table with shifted Lennard-Jones potential it is not 
> comparable to the shift version
> and the energy is not conserved -- ?
> 
> I use a shift function as written in the manual (chapter 4.1.5) -- 
> there must be a factor alpha added in the constants A and B --
> (r1=0).
> 
> The parameters are the same for shift version and shifted user version.
> 
> Has someone an idea why the shifted user potential doesn't work in 
> this way?
> 
> Here is the mdp:
> 
> 
> integrator            = md-vv
> dt                    = 0.0035
> nsteps                    = 1000
> nstxout                    = 1
> nstvout                    = 1
> nstfout                    = 1
> nstlog                    = 1
> ns_type                    = grid
> pbc                    = xyz
> rvdw                    = 3.24
> rlist                    = 3.6
> tcoupl                    = no
> tc-grps                    = System
> tau_t                    = 2.0
> ref_t                    = 127.2717
> vdwtype                    = user;Shift
> rcoulomb            = 3.6;2.24;1.12
> coulombtype            = Cut-off
> rvdw-switch            = 0.0
> 
> energygrps            = bead
> energygrp_table            = bead bead
> 
> 
> Thanks in advance
> Anja
> 

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