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.war...@monash.edu <mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@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-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@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.war...@monash.edu <mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@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-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>] On Behalf Of bharat gupta
> Sent: Wednesday, 28 September 2011 12:48 PM
> To: jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@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
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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 : monu46...@yahoo.com <mailto:monu46...@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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
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