[gmx-users] Re: simulation of protein/water and phosphate ion

[bharat gupta]

it's showing error that certain atoms cannot be settled and these atoms are
of solvent molecules i.e. Water


On Wednesday, September 28, 2011, Dallas Warren <Dallas.Warren at monash.edu>
wrote:
> What is actually blowing up?  The protein or the phosphate ions?  Do the
phosphate ions run OK by themselves in water?
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
nail.
>
>
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of bharat gupta
> Sent: Wednesday, 28 September 2011 12:48 PM
> To: jalemkul at vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion
>
>
>
> Hi,
>
> I tried simulating the system again but this time with 2 phsophate ion and
the charge of the system was neutralized by adding 6 sodium ions . After
minimizing , I equilibrated for 500 ps but I got "LINCS" error around
300ps.  It's happening due to the addition of phosphate ions as I have
simulated my protein in water earlier without any problem. During nvt
quilibration the temperature coupling settings were for Protein and Non
protein groups. Do I have to make groups for Protein and water_ion. Please
comment??
>
> On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> bharat gupta wrote:
>
> HI,
>
> I have tried simulating my protein (GFP) solvated with water molecules and
10 phosphate ions. During the md run step the system starts exploding after
 500 ps. What could be the reason for this . I know this is happening due to
the addition of phosphate ion but I need to study the binding of ions . So,
what shall I do ??
>
>
>
>
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
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>
> Mobile no. - 010-5818-3680
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>
>

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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