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

2011-09-28 Thread Mark Abraham 

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 
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
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
mailto:jalem...@vt.edu>> wrote:
>
> bharat gupta wrote:
>
> HI,
>
> I have tried simulating my protein (

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

2011-09-28 Thread 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 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
>
> +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] *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 
> 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
> >
> > +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] On Behalf Of bharat gupta
> > Sent: Wednesday, 28 September 2011 12:48 PM
> > To: 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 
> 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

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

2011-09-27 Thread 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.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] 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 
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 
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org<mailto:gmx-users@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-requ...@gromacs.org<mailto:gmx-users-requ...@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 : monu46...@yahoo.com<mailto:monu46...@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 : monu46...@yahoo.com<mailto:monu46...@yahoo.com>

-- 
gmx-users mailing listgmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

2011-09-27 Thread Dallas Warren 
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
+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] On 
Behalf Of bharat gupta
Sent: Wednesday, 28 September 2011 12:48 PM
To: 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 
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


--
gmx-users mailing listgmx-users@gromacs.org<mailto:gmx-users@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-requ...@gromacs.org<mailto:gmx-users-requ...@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 : monu46...@yahoo.com<mailto:monu46...@yahoo.com>

-- 
gmx-users mailing listgmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

2011-09-27 Thread bharat gupta 
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  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 listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@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 : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

2011-09-27 Thread Justin A. Lemkul 



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 listgmx-users@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-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists