[gmx-users] restraining Ca2+ ion
jayant.james at gmail.com
Wed Jan 7 01:47:55 CET 2009
Thanks for your suggestions. Please take a look at the mdp file that I am
using. Please suggest any changes that you feel would be adequate if the
electrostatic treatment is poor.
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
title = Yo
cpp = /usr/bin/cpp
define = -DDISRES -DPOSRES
constraints = none
integrator = md
dt = 0.001 ; ps !
nsteps = 1000000 ; total 0.5ns.
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
disre = simple
disre_weighting = conservative
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = Protein Non-Protein
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
On Tue, Jan 6, 2009 at 2:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> jayant james wrote:
>> I have been performing MD simulations of a protein which has 3 ca2+ ions.
>> I find that after 3ns of simulations the ca2+ ions start to drift away. So
>> what would be a good strategy to have the ca2+ in place during the
>> simulations. I would prefer not to use position restraining as this would
>> pin the ca2+ in space hindering the spacial movement of that particular
>> area!! but I am wondering if distance restraining of the ca2+ to the
>> adjacent residues would be fine? or is there any other/better strategy?
>> Awaiting your suggestions.
> This is one of the purposes of distance restraints. Better would be a
> proper model for protein-bound calcium ions. Also, a poor-quality
> electrostatic treatment could be the source of the problem (e.g. a cut-off
> shorter than the distances to nearby negative (partial) charges).
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Jayasundar Jayant James
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users