[gmx-users] Re: simulation of protein/water and phosphate ion
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Sep 29 05:50:20 CEST 2011
On 29/09/2011 9:59 AM, bharat gupta wrote:
> I repeated the nvt equilibration with 500 ps and it was successful ,
> after confirming the temperature graph. But during npt simulation, I
> got the following error:-
You are rearranging the deck chairs on a ship that is already sinking.
You've been given good advice from several people - see
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System.
There's nothing more to be said if you don't go and follow the advice
there. You've got a complex piece of machinery that isn't working for
unknown reasons. Diagnosing what is wrong is hard, but only you have the
information, motivation and resources to do it.
>
> step 131500, will finish Thu Sep 29 01:54:20 2011imb F 2%
> step 131520: Water molecule starting at atom 6981 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: pme.c, line: 538
>
> Fatal error:
> 1 particles communicated to PME node 0 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
>
> Since there are large no. of water molecules after 6981 , it means
> that it is not happening because oh some interaction with phosphate ion.
There is no correlation between atom number and geometric proximity to a
suspect molecule. You have to go and look at the initial structure and
the trajectory.
Mark
> What shall be done to rectify this ??
>
>
> On Wed, Sep 28, 2011 at 12:35 PM, Dallas Warren
> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> wrote:
>
> 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 <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 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
> > 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
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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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>
>
> --
> 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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