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

[Dallas Warren]

And where are these waters?  Close to the phosphate ions?

You really need to be asking more questions, looking at the trajectory file / frames when it blows up, and determining what is actually going on by yourself.

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 1:30 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Re: simulation of protein/water and phosphate ion

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<mailto: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<mailto: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> [mailto: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<mailto: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<mailto: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<http://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
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>
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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<mailto:monu46010 at yahoo.com>

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