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.kuhnh...@physik.uni-halle.de>
To: gmx-users@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.kuhnh...@physik.uni-halle.de>
> Date Wed, 06 Jun 2012 15:07:40 +0200
> To gmx-users@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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