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

[bharat gupta]

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:-

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. What shall
be done to rectify this ??


On Wed, Sep 28, 2011 at 12:35 PM, Dallas Warren <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****
>
> +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>
> 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
> >
> > ========================================
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
> >
> > --
> > 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
> >
> >
>
> --
> 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****
>
> ** **
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110929/ebfe5974/attachment.html>