[gmx-users] restraining Ca2+ ion

[jayant james]

Hi,
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.
Thanks
Jayant James

;           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:
>
>> Hi!
>> 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).
>
> Mark
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-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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