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On 29/09/2011 9:59 AM, bharat gupta wrote:
<blockquote
cite="mid:CAAh+zSWSvtsVj_EgX7Eo_vMH_JTmiq-SNXFiZDH9nW5L3hUEZg@mail.gmail.com"
type="cite">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:-<br>
</blockquote>
<br>
You are rearranging the deck chairs on a ship that is already
sinking. You've been given good advice from several people - see
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System">http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a>.
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.<br>
<br>
<blockquote
cite="mid:CAAh+zSWSvtsVj_EgX7Eo_vMH_JTmiq-SNXFiZDH9nW5L3hUEZg@mail.gmail.com"
type="cite"><br>
step 131500, will finish Thu Sep 29 01:54:20 2011imb F 2% <br>
step 131520: Water molecule starting at atom 6981 can not be
settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.4<br>
Source code file: pme.c, line: 538<br>
<br>
Fatal error:<br>
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.<br>
This usually means that your system is not well equilibrated.<br>
<br>
<br>
Since there are large no. of water molecules after 6981 , it means
that it is not happening because oh some interaction with
phosphate ion. </blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAh+zSWSvtsVj_EgX7Eo_vMH_JTmiq-SNXFiZDH9nW5L3hUEZg@mail.gmail.com"
type="cite">What shall be done to rectify this ??<br>
<br>
<br>
<div class="gmail_quote">On Wed, Sep 28, 2011 at 12:35 PM, Dallas
Warren <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span
style="font-size:11.0pt;color:#1F497D">And where are
these waters? Close to the phosphate ions?</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;color:#1F497D"> </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;color:#1F497D">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.</span></p>
<div class="im">
<p class="MsoNormal"><span
style="font-size:11.0pt;color:#1F497D"> </span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;color:#1F497D">Medicinal
Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;color:#1F497D">Monash
Institute of Pharmaceutical Sciences</span><span
style="font-size:10.0pt;color:#1F497D">, Monash
University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a moz-do-not-send="true"
href="mailto:dallas.warren@monash.edu"
target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;color:#1F497D">+61 3 9903
9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every
problem begins to resemble a nail.</span><span
style="font-size:11.0pt;color:#1F497D">
</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;color:#1F497D"> </span></p>
</div>
<div style="border:none;border-left:solid blue
1.5pt;padding:0cm 0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt">From:</span></b><span
style="font-size:10.0pt"> <a
moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>bharat gupta<br>
<b>Sent:</b> Wednesday, 28 September 2011 1:30
PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Re: simulation of
protein/water and phosphate ion</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
<div class="im">it's showing error that certain atoms
cannot be settled and these atoms are of solvent
molecules i.e. Water
<br>
<br>
<br>
On Wednesday, September 28, 2011, Dallas Warren <<a
moz-do-not-send="true"
href="mailto:Dallas.Warren@monash.edu"
target="_blank">Dallas.Warren@monash.edu</a>>
wrote:<br>
</div>
<div>
<div class="h5">
> What is actually blowing up? The protein or
the phosphate ions? Do the phosphate ions run OK by
themselves in water?<br>
><br>
> <br>
><br>
> Catch ya,<br>
><br>
> Dr. Dallas Warren<br>
><br>
> Medicinal Chemistry and Drug Action<br>
><br>
> Monash Institute of Pharmaceutical Sciences,
Monash University<br>
> 381 Royal Parade, Parkville VIC 3010<br>
> <a moz-do-not-send="true"
href="mailto:dallas.warren@monash.edu"
target="_blank">dallas.warren@monash.edu</a><br>
><br>
> +61 3 9903 9304<br>
> ---------------------------------<br>
> When the only tool you own is a hammer, every
problem begins to resemble a nail.<br>
><br>
> <br>
><br>
> From: <a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>]
On Behalf Of bharat gupta<br>
> Sent: Wednesday, 28 September 2011 12:48 PM<br>
> To: <a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>;
Discussion list for GROMACS users<br>
> Subject: Re: [gmx-users] Re: simulation of
protein/water and phosphate ion<br>
><br>
> <br>
><br>
> Hi,<br>
><br>
> 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??<br>
><br>
> On Tue, Sep 27, 2011 at 7:09 PM, Justin A.
Lemkul <<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>
wrote:<br>
><br>
> bharat gupta wrote:<br>
><br>
> HI,<br>
><br>
> 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 ??<br>
><br>
> <br>
><br>
> <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System"
target="_blank">
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a><br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> |
(540) 231-9080<br>
> <a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
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><br>
> --<br>
> Bharat<br>
> Ph.D. Candidate<br>
> Room No. : 7202A, 2nd Floor<br>
> Biomolecular Engineering Laboratory<br>
> Division of Chemical Engineering and Polymer
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> Pusan National University<br>
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> <br>
<br>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
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<p class="MsoNormal">Mobile no. - 010-5818-3680<br>
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href="mailto:monu46010@yahoo.com"
target="_blank">monu46010@yahoo.com</a></p>
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-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343
<div>
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