Re: [gmx-users] Range checking error

[Justin A. Lemkul]

011013021-Jyotsna wrote:


Dear all,

I am simulating a protein along with a ligand molecule. The ligand 
molecule is modeled as per the literature. The ligand molecule consists 
of FE and S alone and in addition to that it is covalently bonded with 
the enzyme's cys residue. So I have modeled my ligand FE4S4 with SG and 
CB atoms of cystine. I have included only bonded terms in my forcefield 
for my ligand (since I do not know other terms like angle and dihedral 
angles force constants etc) and the article does not mention these.


Now the problem is, when I try to run energy minimization , I encounter  
"Range checking error:" and the detailed error is pasted below. So I 
suspect this error is due to inadequate force field data like angles and 
dihedrals. Or is it caused by some other factor?.But one thing I am sure 


More likely the underlying physics is unreasonable.  See here:

http://www.gromacs.org/Documentation/Errors#Range_Checking_error

of is , when I simulate my system without the ligand, the error 
disappears. I am unable to find any answer to this query in the forum.


Kindly extend your help this time as you always do.


#
Steepest Descents:
   Tolerance (Fmax)   =  2.0e+02
   Number of steps= 5000
Warning: 1-4 interaction between 2446 and 2468 at distance 6.079 which 
is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step=0, Dmax= 1.0e-02 nm, Epot=  nan Fmax= 1.71540e+115, 
atom= 2452


You should have seen these errors in the list archive if you did a search.  Your 
system is clearly blowing up (see link above).  Your Fmax is essentially 
infinite, which is usually due to extreme atomic overlap, which should be clear 
in the input structure.  Otherwise, mdrun is giving you clues about atoms 2446 
and 2468 - start investigating there.



---
Program mdrun_d, VERSION 4.0
Source code file: nsgrid.c, line: 357



I would also encourage you to upgrade to the latest version (4.0.7); it will not 
fix your problem, but there have certainly been some important bug fixes related 
to stability and usability that will make your life easier :)


-Justin


Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 4096 ]

# 



Thank You
Jyotsna














On Wed, 03 Feb 2010 22:42:09 +1100
 Mark Abraham  wrote:

*This message was transferred with a trial version of CommuniGate(r) Pro*


- Original Message -
From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu>
Date: Wednesday, February 3, 2010 21:48
Subject: Re: [gmx-users] H2 topology
To: Discussion list for GROMACS users 



Dear David,

Thanks for your reply.  From your reply, I get the impression that 
the bond length of my hydrogen molecule gets adjusted duing 
minimization of the whole system ( protien+water+ inserted hydrogen 
molecule). But the issue impending is the insertion of the hydrogen 
molecule itself into the protein+water box created in previous step. 
For insertion/addition of hydrogen molecules I used the command:


genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top –ci h2.gro 
–nmol 100


What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when 
there's no water, and then solvate *afterwards*.


Or, generate solvent, and get a list of 100 random numbers in the 
right range, manually delete those water molecules to create 
interstices, update your [molecules] section, then use genconf -ci and 
equilibrate carefully to fix the density.


Or, generate solvent for a box somewhat smaller than the one you want, 
use editconf -scale to scale the coordinates up to create interstices, 
use genconf -ci and then minimize really gently to fix all the bond 
lengths, and equilibrate carefully to fix the density.


Mark

 It reports to me the inability to add any of the hydrogen molecules, 
ie it adds 0 molecules out of 100 requested.

###error
Reading molecule configuration
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
Containing 3 atoms in 1 residue
Initialising van der waals distances...
Try 999
Added 0 molecules (out of 100 requested) of H2
Writing ge

[gmx-users] Range checking error

[011013021-Jyotsna]

Dear all,

I am simulating a protein along with a ligand molecule. 
The ligand molecule is modeled as per the literature. The 
ligand molecule consists of FE and S alone and in addition 
to that it is covalently bonded with the enzyme's cys 
residue. So I have modeled my ligand FE4S4 with SG and CB 
atoms of cystine. I have included only bonded terms in my 
forcefield for my ligand (since I do not know other terms 
like angle and dihedral angles force constants etc) and 
the article does not mention these.


Now the problem is, when I try to run energy minimization 
, I encounter  "Range checking error:" and the detailed 
error is pasted below. So I suspect this error is due to 
inadequate force field data like angles and dihedrals. Or 
is it caused by some other factor?.But one thing I am sure 
of is , when I simulate my system without the ligand, the 
error disappears. I am unable to find any answer to this 
query in the forum.


Kindly extend your help this time as you always do.


#
Steepest Descents:
   Tolerance (Fmax)   =  2.0e+02
   Number of steps= 5000
Warning: 1-4 interaction between 2446 and 2468 at distance 
6.079 which is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp 
file

or with user tables increase the table size
Step=0, Dmax= 1.0e-02 nm, Epot=  nan Fmax= 
1.71540e+115, atom= 2452

---
Program mdrun_d, VERSION 4.0
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each 
particle to a grid
based on its coordinates. If your system contains 
collisions or parameter
errors that give particles very high velocities you might 
end up with some
coordinates being +-Infinity or NaN (not-a-number). 
Obviously, we cannot
put these on a grid, so this is usually where we detect 
those errors.
Make sure your system is properly energy-minimized and 
that the potential

energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been 
within [ 0 .. 4096 ]


#

Thank You
Jyotsna














On Wed, 03 Feb 2010 22:42:09 +1100
 Mark Abraham  wrote:
*This message was transferred with a trial version of 
CommuniGate(r) Pro*



- Original Message -
From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu>
Date: Wednesday, February 3, 2010 21:48
Subject: Re: [gmx-users] H2 topology
To: Discussion list for GROMACS users 





Dear David,

Thanks for your reply.  From your reply, I get the 
impression that the bond length of my hydrogen molecule 
gets 
adjusted duing minimization of the whole system ( 
protien+water+ 
inserted hydrogen molecule). But the issue impending is 
the 
insertion of the hydrogen molecule itself into the 
protein+water 
box created in previous step. For insertion/addition of 
hydrogen 
molecules I used the command:


genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top 
–ci 
h2.gro –nmol 100


What about a two-stage process? Do genbox -ci h2.gro 
-nmol 100 when there's no water, and then solvate 
*afterwards*.


Or, generate solvent, and get a list of 100 random 
numbers in the right range, manually delete those water 
molecules to create interstices, update your [molecules] 
section, then use genconf -ci and equilibrate carefully 
to fix the density.


Or, generate solvent for a box somewhat smaller than the 
one you want, use editconf -scale to scale the 
coordinates up to create interstices, use genconf -ci and 
then minimize really gently to fix all the bond lengths, 
and equilibrate carefully to fix the density.


Mark

 It reports to me the inability to add any of the 
hydrogen 
molecules, ie it adds 0 molecules out of 100 requested.

###error
Reading molecule configuration
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
Containing 3 atoms in 1 residue
Initialising van der waals distances...
Try 999
Added 0 molecules (out of 100 requested) of H2
Writing generated configuration to 2frv.solv.gro

Back Off! I just backed up 2frv.solv.gro to 
./#2frv.solv.gro.1#

PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE

Output configuration contains 8340 atoms in 977 residues
Volume : 1299.08 (nm^3)
Density : 143.043 (g/l)
Number of SOL molecules: 186

Processing topology
Removing line #40 'SOL 39308' from topology file 
(2frv.top)

error end###
How do i rectify this problem?
 I suspect the problem is due to the bond length of the 
hydrogen molecule that I created with 1.66A distance ( 
as 
described in my previous post) and the fact that the gap 
between 
the solvent molecules (in my case , water) is not big 
enough to 
accomodate the H2 molecules(as I h

Re: [gmx-users] Range checking error: only on double precision

[Jack Shultz]

I guess its the amber03 force field I'm having issues with. The
lysozyme tutorial works if I use -ff G43a2
Thanks

Jack

On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul  wrote:
>
> Well, several tutorials use lysozyme, PDB 1AKI.  I would also recommend not
> using ffamber if you are running automated tests, since there are quirks
> with requiring specific nomenclature (for lysine, histidine, terminal
> residues, etc).
>
> -Justin
>
> Jack Shultz wrote:
>>
>> Justin,
>>
>> Can you suggest any pdb files I could use that are more simple? I've
>> been trying to use files from tutorials but it seems like are always
>> problematic.
>>
>> Jack
>>
>> On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul  wrote:
>>>
>>> Jack Shultz wrote:

 Hello,

 I just wanted to compare results between single and double precision.
 I reused the same parameters. Single works. Double caused errors on
 mdrun. Any idea why?

 http://hydrogenathome.org/result.php?resultid=1292662

>>> I don't know why any of that worked at all.  You've got missing atoms and
>>> inconsistent naming (LYSH should be LYP if you really want a protonated
>>> lysine under the Amber ports, etc).  Did you give pdb2gmx -missing?
>>>  Otherwise, topology generation should have failed.
>>>
>>> Especially troublesome:
>>>
>>> System has non-zero total charge: -2.309866e+01
>>>
>>> I would suggest running tests on a physically realistic system that has
>>> all
>>> atoms present and an integer charge.  Maybe single precision somehow
>>> overcame these topology problems, but I wouldn't trust any of the
>>> results.
>>>
>>> -Justin
>>>
 ---
 Program mdrun, VERSION 4.0.3
 Source code file: nsgrid.c, line: 357

 Range checking error:
 Explanation: During neighborsearching, we assign each particle to a grid
 based on its coordinates. If your system contains collisions or
 parameter
 errors that give particles very high velocities you might end up with
 some
 coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
 put these on a grid, so this is usually where we detect those errors.
 Make sure your system is properly energy-minimized and that the
 potential
 energy seems reasonable before trying again.

 Variable ci has value -2147483648. It should have been within [ 0 .. 300
 ]



>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> 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-us...@gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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-us...@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
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Re: [gmx-users] Range checking error: only on double precision

[Justin A. Lemkul]

Well, several tutorials use lysozyme, PDB 1AKI.  I would also recommend not 
using ffamber if you are running automated tests, since there are quirks with 
requiring specific nomenclature (for lysine, histidine, terminal residues, etc).


-Justin

Jack Shultz wrote:

Justin,

Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
problematic.

Jack

On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul  wrote:


Jack Shultz wrote:

Hello,

I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?

http://hydrogenathome.org/result.php?resultid=1292662


I don't know why any of that worked at all.  You've got missing atoms and
inconsistent naming (LYSH should be LYP if you really want a protonated
lysine under the Amber ports, etc).  Did you give pdb2gmx -missing?
 Otherwise, topology generation should have failed.

Especially troublesome:

System has non-zero total charge: -2.309866e+01

I would suggest running tests on a physically realistic system that has all
atoms present and an integer charge.  Maybe single precision somehow
overcame these topology problems, but I wouldn't trust any of the results.

-Justin


---
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]




--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
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or send it to gmx-users-requ...@gromacs.org.
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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Range checking error: only on double precision

[Jack Shultz]

Justin,

Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
problematic.

Jack

On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul  wrote:
>
>
> Jack Shultz wrote:
>>
>> Hello,
>>
>> I just wanted to compare results between single and double precision.
>> I reused the same parameters. Single works. Double caused errors on
>> mdrun. Any idea why?
>>
>> http://hydrogenathome.org/result.php?resultid=1292662
>>
>
> I don't know why any of that worked at all.  You've got missing atoms and
> inconsistent naming (LYSH should be LYP if you really want a protonated
> lysine under the Amber ports, etc).  Did you give pdb2gmx -missing?
>  Otherwise, topology generation should have failed.
>
> Especially troublesome:
>
> System has non-zero total charge: -2.309866e+01
>
> I would suggest running tests on a physically realistic system that has all
> atoms present and an integer charge.  Maybe single precision somehow
> overcame these topology problems, but I wouldn't trust any of the results.
>
> -Justin
>
>> ---
>> Program mdrun, VERSION 4.0.3
>> Source code file: nsgrid.c, line: 357
>>
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle to a grid
>> based on its coordinates. If your system contains collisions or parameter
>> errors that give particles very high velocities you might end up with some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>> put these on a grid, so this is usually where we detect those errors.
>> Make sure your system is properly energy-minimized and that the potential
>> energy seems reasonable before trying again.
>>
>> Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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-us...@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
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Re: [gmx-users] Range checking error: only on double precision

[Justin A. Lemkul]

Jack Shultz wrote:

Hello,

I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?

http://hydrogenathome.org/result.php?resultid=1292662



I don't know why any of that worked at all.  You've got missing atoms and 
inconsistent naming (LYSH should be LYP if you really want a protonated lysine 
under the Amber ports, etc).  Did you give pdb2gmx -missing?  Otherwise, 
topology generation should have failed.


Especially troublesome:

System has non-zero total charge: -2.309866e+01

I would suggest running tests on a physically realistic system that has all 
atoms present and an integer charge.  Maybe single precision somehow overcame 
these topology problems, but I wouldn't trust any of the results.


-Justin


---
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]





--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] Range checking error: only on double precision

[Jack Shultz]

Hello,

I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?

http://hydrogenathome.org/result.php?resultid=1292662

---
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
___
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Re: [gmx-users] Range checking error

[Mark Abraham]

[EMAIL PROTECTED] wrote:

My initial input file is a model which was generated using Modeller, and
it is a part of the original structure. I am considering fragments of a
particular structure for my analysis. Could this be a possible problem for
running a simulation?? I suppose there is a problem when I try to convert
this PDB file into a .gro file. But I have no clue as to what the possible
problem could be. The format of my input PDB file is correct.


Well, you don't need a .gro file - see 
http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file


Chopping something into fragments is a great way to make chemical 
nonsense, but pdb2gmx and grompp will often give you warnings and errors 
about such things. Read them carefully and pay attention!



Also I tried to run a job for the original PDB structure which worked
perfectly fine.


Well that means your problem came with something you did...

Mark
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Re: [gmx-users] Range checking error

[namita]

My initial input file is a model which was generated using Modeller, and
it is a part of the original structure. I am considering fragments of a
particular structure for my analysis. Could this be a possible problem for
running a simulation?? I suppose there is a problem when I try to convert
this PDB file into a .gro file. But I have no clue as to what the possible
problem could be. The format of my input PDB file is correct.

Also I tried to run a job for the original PDB structure which worked
perfectly fine.

> [EMAIL PROTECTED] wrote:
>> Dear members
>>
>> I happened to get an error which is as follows :
>
>> Range checking error:
>
>> I think it is a problem with energy minimisation and neutralising the
>> system. However I tried many ways to solve the issue, it still seems to
>> give me the same error. Could anyone suggest what could be the possible
>> cause of this error.
>
> There's a problem with either your original structure, or the topology
> with which you're trying to describe its physics. You can find some
> clues here http://wiki.gromacs.org/index.php/Errors#mdrun for causes for
> similar problems, but without more information, we're guessing.
>
> Mark
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Re: [gmx-users] Range checking error

[Mark Abraham]

[EMAIL PROTECTED] wrote:

Dear members

I happened to get an error which is as follows :



Range checking error:



I think it is a problem with energy minimisation and neutralising the
system. However I tried many ways to solve the issue, it still seems to
give me the same error. Could anyone suggest what could be the possible
cause of this error.


There's a problem with either your original structure, or the topology 
with which you're trying to describe its physics. You can find some 
clues here http://wiki.gromacs.org/index.php/Errors#mdrun for causes for 
similar problems, but without more information, we're guessing.


Mark
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[gmx-users] Range checking error

[namita]

Dear members

I happened to get an error which is as follows :


Error on node 17, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 17 out of 32

gcq#106: "Step Aside, Butch" (Pulp Fiction)

node26:19.MPID_CH_Abort: node26:19.Aborting program!
node26:17.MPID_CH_Abort: node26:17.Aborting program!
node26:16.MPID_CH_Abort: node26:16.Aborting program!
node26:18.MPID_Abort: node26:18.MPI Abort by user Aborting program !
node26:18.MPID_CH_Abort: node26:18.Aborting program!
---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 658503 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---

"Step Aside, Butch" (Pulp Fiction)

Error on node 16, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 16 out of 32

gcq#106: "Step Aside, Butch" (Pulp Fiction)

I think it is a problem with energy minimisation and neutralising the
system. However I tried many ways to solve the issue, it still seems to
give me the same error. Could anyone suggest what could be the possible
cause of this error.

Thanks in advance
Sincerely
Namitha

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Re: [gmx-users] Range checking error

[Mark Abraham]

SeungPyo Hong wrote:

Dear gmx-users,

I run MD for a protein molecule solvated with water molecules.
Until now it works well, however strangely they started to crash, I 
don't know the reason.

So, if anyone have similar problem please let me know the solution.
It seems like that NPT system might cause some problems.


You need to prepare your system better, and/or equilibrate more gently. 
See http://wiki.gromacs.org/index.php/blowing_up and links thereon. Pay 
attention to any warning messages from grompp.


Mark
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[gmx-users] Range checking error

[SeungPyo Hong]

Dear gmx-users,

I run MD for a protein molecule solvated with water molecules.
Until now it works well, however strangely they started to crash, I don't
know the reason.
So, if anyone have similar problem please let me know the solution.
It seems like that NPT system might cause some problems.

Also, when I continue MD further, it works.
(Sometimes simulation crashes after 1 ns, but sometimes it crashes only
after 100 ps.)
Then, can I use those results for further studies?

This is the mdp file:
integrator  = md
nsteps  = 150
dt  = 0.002
nstlist = 10
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = Berendsen
tc-grps = protein non-protein
tau-t   = 0.1 0.1
ref-t   = 310 310
pcoupl  = Berendsen
pcoupltype  = isotropic
tau-p   = 1
ref-p   = 1.0
compressibility = 4.5e-5
constraints = all-bonds
constraint_algorithm = lincs
nstxout = 1000
nstvout = 1
nstxtcout   = 100
nstenergy   = 100
; Generate velocity is on at 300 K
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529

This is the error message:
---
Program mdrun_mpi_d, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 3185. It should have been within [ 0 .. 3072 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---

"Interfacing Space and Beyond..." (P. J. Harvey)

Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi_d on CPU 1 out of 16

gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)

[1] MPI Abort by user Aborting program !
[1] Aborting program!
---
-- 
--
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
[EMAIL PROTECTED]
[EMAIL PROTECTED]
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[gmx-users] Range checking error

[Yanzi Zhou]

Dear Gromacs-Users,
Is there anybody have met such problem before?

I did NTP simulation for POPE system downloaded from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies.
It can run for even 10 ns with single precision GROMACS on many
processors or with double precision GROMACS on 1 or 2 processors, but
crash at about 100ps with double
GROMACS on more than 2 processors. The same thing didn't happen for a
NTV simulation.
I don't think it can be ascribed to the initial structure, because I
used the same initial structure and input files for tests. Which one do
you prefer for MD simulation, single or double precision?

Here is the error message:

Program mdrun_mpi_d, VERSION 3.3.2
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 4421. It should have been within [ 0 .. 4212 ]

---

I compiled GROMACS on Linux x86_64 with mvapich-0.9.9, this is how I
complied it:
#!/bin/csh -f

setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv MPICC mpicc

setenv CFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip"
setenv CXXFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip"
setenv FFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip"

setenv CPPFLAGS "-I/home/yz30/Intel/FFTW-3.1.2-Lib/include"
setenv LDFLAGS "-L/home/yz30/Intel/FFTW-3.1.2-Lib/lib -L/usr/X11R6/lib64"

./configure --prefix=/scratch/yz30/Intel/Gromacs-3.3.2-FFTW3
--enable-double --with-fft=fftw3 \
--enable-mpi --program-suffix=_mpi_d --disable-nice


Thanks in advance.
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Re: [gmx-users] Range checking error

[Yanzi Zhou]

I did MD simulation for lipid. I downloaded the pre-equilibrated 
structure and parameters from 
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I 
can do 5 ns NTP simulation with single precision, but it can't go on 
with double precision.
I also tried the DPPC from the benchmarks of Gromacs. I first did the 
NTV simulation for 500 ps, and then do NTP simulation using PME, but 
crashed.



Mark Abraham wrote:

Yanzi Zhou wrote:

Thank you.
I recompiled the software with gcc, but my job still crashed at about 
170ps. I tried 1 ns simulation for 1PGB in water downloaded from 
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be 
finished. But when I tried to do NTP simulation of DPPC from the 
benchmarks of Gromacs, my job died on 6 processes with double 
precision gromacs.  I found the job crashed when I:

do NTP simulation for a large system, and
use PME
on more than two processors with double precision gromacs.


Make sure your system is properly energy-minimized and that the 
potential


energy seems reasonable before trying again.


What have you done to check that your system preparation protocol is 
reasonable?


Mark
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Re: [gmx-users] Range checking error

[Mark Abraham]

Yanzi Zhou wrote:

Thank you.
I recompiled the software with gcc, but my job still crashed at about 
170ps. I tried 1 ns simulation for 1PGB in water downloaded from 
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. 
But when I tried to do NTP simulation of DPPC from the benchmarks of 
Gromacs, my job died on 6 processes with double precision gromacs.  I 
found the job crashed when I:

do NTP simulation for a large system, and
use PME
on more than two processors with double precision gromacs.


Make sure your system is properly energy-minimized and that the 
potential


energy seems reasonable before trying again.


What have you done to check that your system preparation protocol is 
reasonable?


Mark
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Re: [gmx-users] Range checking error

[Yanzi Zhou]

Thank you.
I recompiled the software with gcc, but my job still crashed at about 
170ps. I tried 1 ns simulation for 1PGB in water downloaded from 
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. 
But when I tried to do NTP simulation of DPPC from the benchmarks of 
Gromacs, my job died on 6 processes with double precision gromacs.  I 
found the job crashed when I:

do NTP simulation for a large system, and
use PME
on more than two processors with double precision gromacs.


David van der Spoel wrote:

Yanzi Zhou wrote:

Dear Gromacs-Users,

Can anybody help me?

When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes
with double precision gromacs compiled by Intel compiler on x86_64
GNU/Linux, it was crashing at about 100 ps with a message:

---

Program mdrun_mpi_d, VERSION 3.3.2

Source code file: nsgrid.c, line: 226

Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or 
parameter


errors that give particles very high velocities you might end up with 
some


coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the 
potential


energy seems reasonable before trying again.

Variable ci has value 4421. It should have been within [ 0 .. 4212 ]

---


But it can be finished when I use 1 or 2 processes, or use cut-off for
electrostatics instead of PME, or for a NVT system, or with single
precision gromacs. I have noticed the bug #167 on Bugzilla, and modified
routine stat.c, but it did no help, and actually I didn't write to XTC
file. Maybe, there are still bugs for double precision gromacs?


More likely the compiler. Please retry with gcc.




Thanks for any help.

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Re: [gmx-users] Range checking error

[David van der Spoel]

Yanzi Zhou wrote:

Dear Gromacs-Users,

Can anybody help me?

When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes
with double precision gromacs compiled by Intel compiler on x86_64
GNU/Linux, it was crashing at about 100 ps with a message:

---

Program mdrun_mpi_d, VERSION 3.3.2

Source code file: nsgrid.c, line: 226

Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or parameter

errors that give particles very high velocities you might end up with some

coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the potential

energy seems reasonable before trying again.

Variable ci has value 4421. It should have been within [ 0 .. 4212 ]

---


But it can be finished when I use 1 or 2 processes, or use cut-off for
electrostatics instead of PME, or for a NVT system, or with single
precision gromacs. I have noticed the bug #167 on Bugzilla, and modified
routine stat.c, but it did no help, and actually I didn't write to XTC
file. Maybe, there are still bugs for double precision gromacs?


More likely the compiler. Please retry with gcc.




Thanks for any help.

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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Range checking error

[Yanzi Zhou]

Dear Gromacs-Users,

Can anybody help me?

When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes
with double precision gromacs compiled by Intel compiler on x86_64
GNU/Linux, it was crashing at about 100 ps with a message:

---

Program mdrun_mpi_d, VERSION 3.3.2

Source code file: nsgrid.c, line: 226

Range checking error:

Explanation: During neighborsearching, we assign each particle to a grid

based on its coordinates. If your system contains collisions or parameter

errors that give particles very high velocities you might end up with some

coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot

put these on a grid, so this is usually where we detect those errors.

Make sure your system is properly energy-minimized and that the potential

energy seems reasonable before trying again.

Variable ci has value 4421. It should have been within [ 0 .. 4212 ]

---


But it can be finished when I use 1 or 2 processes, or use cut-off for
electrostatics instead of PME, or for a NVT system, or with single
precision gromacs. I have noticed the bug #167 on Bugzilla, and modified
routine stat.c, but it did no help, and actually I didn't write to XTC
file. Maybe, there are still bugs for double precision gromacs?


Thanks for any help.

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Re: [gmx-users] "Range checking error" issue

[David van der Spoel]

From this point of view things seem to be much more clear to me i.e.

since the z
coordinates is shrinking, the Grid size gets updated to the new value
10x12x12
(initial value was 10x12x13!!!).

This might lead to the "Range checking error" if this situation is not
handled
properly by the gmx code.

MG.
As I said before, retry with gcc. Compilers suck big time, they have a 
billion times more bugs than gromacs.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] "Range checking error" issue

[Matteo Guglielmi]

David van der Spoel wrote:
> Matteo Guglielmi wrote:
>> Mark Abraham wrote:
>>> Matteo Guglielmi wrote:
 I did what you suggest and even more, I decreased the timestep to
 0.001

 Well the problem doesn't go away.

 I've been reading mails from this discussion list... I'm not the only
 who's experiencing this kind of problem (ci variable range error)...
 actually few gmx users suggest it comes only from parallel runs which
 is my case BTW.
>>> I've seen it most often when equilibration hasn't happened properly,
>>> but you'd think 1.5ns would be enough to avoid a crash.
>>>
 I'm running parallel runs on different clusters... it's happening
 everywhere.
>>> Do serial runs do it?
>>>
>>> Have you looked at your trajectory visually to see where things start
>>> going wrong?
>>>
>>> Mark
>>> ___
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>>>
>> I did no try any serial run yet... trajectory looks fine... but log
>> files might explain
>> why parallel runs keep crashing.
>>
>> Usually I run gromacs on a dual  Xeon 5140 cpus machine (2x2-cores) in
>> double precision.
>>
>> I did compile gromacs using the intel compilers - 9.1 series:
>>  
>> [EMAIL PROTECTED] ~]$ icc -V
>> Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
>> 9.1Build 20070320 Package ID: l_cc_c_9.1.049
>> Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.
>>
>> [EMAIL PROTECTED] ~]$ icpc -V
>> Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
>> 9.1Build 20070320 Package ID: l_cc_c_9.1.049
>> Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.
>>
>> [EMAIL PROTECTED] ~]$ ifort -V
>> Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
>> 9.1Build 20070320 Package ID: l_fc_c_9.1.045
>> Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.
>>
> an't post? Read http://www.gromacs.org/mailing_lists/users.php
> try again with gcc in that case. if that gives the same behavior then
> please submit a bugzilla.
>

I did post here (gmx-users-list) because the problem I'm currently
experiencing
with gromacs could be related to my input file set-up... anyway, you are
right.

What I noticed right now in my simulation is that the volume of the box
shrinks.
(water molecules not equilibrated)

I've also noticed that among the tree coordinates, z shrinks a bit
faster than x and y.

>From this point of view things seem to be much more clear to me i.e.
since the z
coordinates is shrinking, the Grid size gets updated to the new value
10x12x12
(initial value was 10x12x13!!!).

This might lead to the "Range checking error" if this situation is not
handled
properly by the gmx code.

MG.
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Re: [gmx-users] "Range checking error" issue

[David van der Spoel]

Matteo Guglielmi wrote:

Mark Abraham wrote:

Matteo Guglielmi wrote:

I did what you suggest and even more, I decreased the timestep to 0.001

Well the problem doesn't go away.

I've been reading mails from this discussion list... I'm not the only
who's experiencing this kind of problem (ci variable range error)...
actually few gmx users suggest it comes only from parallel runs which
is my case BTW.

I've seen it most often when equilibration hasn't happened properly,
but you'd think 1.5ns would be enough to avoid a crash.


I'm running parallel runs on different clusters... it's happening
everywhere.

Do serial runs do it?

Have you looked at your trajectory visually to see where things start
going wrong?

Mark
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I did no try any serial run yet... trajectory looks fine... but log
files might explain
why parallel runs keep crashing.

Usually I run gromacs on a dual  Xeon 5140 cpus machine (2x2-cores) in
double precision.

I did compile gromacs using the intel compilers - 9.1 series:
 
[EMAIL PROTECTED] ~]$ icc -V

Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[EMAIL PROTECTED] ~]$ icpc -V
Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[EMAIL PROTECTED] ~]$ ifort -V
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_fc_c_9.1.045
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.


an't post? Read http://www.gromacs.org/mailing_lists/users.php
try again with gcc in that case. if that gives the same behavior then 
please submit a bugzilla.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] "Range checking error" issue

[Matteo Guglielmi]

Mark Abraham wrote:
> Matteo Guglielmi wrote:
>> I did what you suggest and even more, I decreased the timestep to 0.001
>>
>> Well the problem doesn't go away.
>>
>> I've been reading mails from this discussion list... I'm not the only
>> who's experiencing this kind of problem (ci variable range error)...
>> actually few gmx users suggest it comes only from parallel runs which
>> is my case BTW.
>
> I've seen it most often when equilibration hasn't happened properly,
> but you'd think 1.5ns would be enough to avoid a crash.
>
>> I'm running parallel runs on different clusters... it's happening
>> everywhere.
>
> Do serial runs do it?
>
> Have you looked at your trajectory visually to see where things start
> going wrong?
>
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
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>
I did no try any serial run yet... trajectory looks fine... but log
files might explain
why parallel runs keep crashing.

Usually I run gromacs on a dual  Xeon 5140 cpus machine (2x2-cores) in
double precision.

I did compile gromacs using the intel compilers - 9.1 series:
 
[EMAIL PROTECTED] ~]$ icc -V
Intel(R) C Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[EMAIL PROTECTED] ~]$ icpc -V
Intel(R) C++ Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_cc_c_9.1.049
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[EMAIL PROTECTED] ~]$ ifort -V
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
9.1Build 20070320 Package ID: l_fc_c_9.1.045
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

 compilatition setup detalis ###
export F77='ifort'
export CC='icc'
export CFLAGS='-axT -unroll -ip -O3'
export FFLAGS='-axT -unroll -ip -O3'
export CPPFLAGS="-I${HOME}/Software/fftw-3.1.2/include"
export LDFLAGS="-L${HOME}/Software/fftw-3.1.2/lib"
./configure --enable-double --with-fft=fftw3 --program-suffix=''
--enable-fortran --enable-threads --prefix=${HOME}/Software/gromacs-3.3.1
make
make install
make distclean
./configure  --enable-mpi --enable-double --with-fft=fftw3
--program-suffix='' --enable-fortran --enable-threads
--prefix=${HOME}/Software/gromacs-3.3.1
make mdrun
make install-mdrun
#

I use openMPI 1.2.1 which was compiled with the same intel compilers
I've shown before.

All my systems were pre-geometry optimized:
emtol = 70
integrator = steep
constraints = none

 md0.log ###
[EMAIL PROTECTED] ~]$ cat md0.log | grep Grid
   ns_type  = Grid
Grid: 10 x 12 x 13 cells

 md1.log ###
[EMAIL PROTECTED] ~]$ cat md1.log | grep Grid
Grid: 10 x 12 x 13 cells
Grid: 10 x 12 x 12 cells

[EMAIL PROTECTED] ~]$ tail -40 md1.log
   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.009211   7638   7640   0.001295
After LINCS 0.00  10707  10709   0.00

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.008704   9341   9344   0.001308
After LINCS 0.00  12623  12625   0.00

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.009517   8162   8163   0.001276
After LINCS 0.00   8355   8357   0.00

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.009805   7638   7640   0.001325
After LINCS 0.00  10207  10210   0.00

   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.009253  12747  12750   0.001259
After LINCS 0.00   8377   8379   0.00

Grid: 10 x 12 x 12 cells
---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 1476. It should have been within [ 0 .. 1440 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---

"Ease Myself Into the Body Bag" (P.J. Harvey)
###

Re: [gmx-users] "Range checking error" issue

[Mark Abraham]

Matteo Guglielmi wrote:

I did what you suggest and even more, I decreased the timestep to 0.001

Well the problem doesn't go away.

I've been reading mails from this discussion list... I'm not the only
who's experiencing this kind of problem (ci variable range error)...
actually few gmx users suggest it comes only from parallel runs which
is my case BTW.


I've seen it most often when equilibration hasn't happened properly, but 
you'd think 1.5ns would be enough to avoid a crash.



I'm running parallel runs on different clusters... it's happening
everywhere.


Do serial runs do it?

Have you looked at your trajectory visually to see where things start 
going wrong?


Mark
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Re: [gmx-users] "Range checking error" issue

[Matteo Guglielmi]

David van der Spoel wrote:
> Matteo Guglielmi wrote:
>> Hello world,
>>
>> the following is my input file:
>>
>> 
>> title= 2masn
>> cpp  = /usr/bin/cpp
>> define   = -DPOSRES
>> integrator   = md
>> tinit= 0
>> dt   = 0.002
>> nsteps   = 150
>> init_step= 0
>> comm_mode= Angular
>> nstcomm  = 1
>> comm_grps= Pore
>> nstxout  = 25
>> nstvout  = 25
>> nstfout  = 25
>> nstcheckpoint= 1000
>> nstlog   = 2500
>> nstxtcout= 2500
>> xtc_grps = System
>> energygrps   = Pore Membrane Ions Water
>> nstenergy= 2500
>> nstlist  = 5
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 1.0
>> coulombtype  = PME
>> rcoulomb = 1.0
>> vdwtype  = Cut-off
>> rvdw = 1.4
>> fourier_nx   = 88
>> fourier_ny   = 88
>> fourier_nz   = 88
>> pme_order= 4
>> ewald_rtol   = 1e-5
>> ewald_geometry   = 3d
>> optimize_fft = yes
>> tcoupl   = berendsen
>> tc_grps  = Solute Solvent
>> tau_t= 0.10.4
>> ref_t= 300300
>> pcoupl   = berendsen
>> pcoupltype   = anisotropic
>> tau_p= 0.5  0.5  0.5  0.50.50.5
>> compressibility  = 4.53e-5  4.53e-5  4.53e-5  0.00.00.0
>> ref_p= 1.0251.0251.0251.025  1.025 
>> 1.025
>> gen_vel  = yes
>> gen_temp = 300
>> gen_seed = 173529
>> constraints  = all-bonds
>> constraint_algorithm = lincs
>> unconstrained_start  = no
>> lincs_order  = 4
>> lincs_iter   = 2
>> lincs_warnangle  = 30
>> 
>>
>> and way after the very beginning of this simulation (~1.5ns) I always
>> get this error message:
>>
>> ##
>>Rel. Constraint Deviation:  Maxbetween atoms RMS
>>Before LINCS 0.032676  17797  17799   0.003970
>> After LINCS 0.04  17162  17169   0.00
>>
>> Grid: 10 x 11 x 12 cells
>> Grid: 10 x 12 x 12 cells
>> Grid: 10 x 11 x 12 cells
>> Grid: 10 x 12 x 12 cells
>> Grid: 10 x 11 x 12 cells
>> Grid: 10 x 12 x 12 cells
>> Grid: 10 x 11 x 12 cells
>> Grid: 10 x 12 x 12 cells
>> Grid: 10 x 11 x 12 cells
>> ---
>> Program mdrun_mpi, VERSION 3.3.1
>> Source code file: nsgrid.c, line: 226
>>
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle to a grid
>> based on its coordinates. If your system contains collisions or
>> parameter
>> errors that give particles very high velocities you might end up with
>> some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>> put these on a grid, so this is usually where we detect those errors.
>> Make sure your system is properly energy-minimized and that the
>> potential
>> energy seems reasonable before trying again.
>>
>> Variable ci has value 1434. It should have been within [ 0 .. 1320 ]
>> Please report this to the mailing list (gmx-users@gromacs.org)
>> ---
>> #
>>
>> Is my input file so bad?
>
> I would increase tau_p to at least 5 ps for anisotropic coupling.
>
>>
>> (I've seen people using lincs with 5fs time step...)
>>
>> Thanks for any useful suggestion,
>> MG.
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
I did what you suggest and even more, I decreased the timestep to 0.001

Well the problem doesn't go away.

I've been reading mails from this discussion list... I'm not the only
who's experiencing this kind of problem (ci variable range error)...
actually few gmx users suggest it comes only from parallel runs which
is my case BTW.

I'm running parallel runs on different clusters... it's happening
everywhere.
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Re: [gmx-users] "Range checking error" issue

[David van der Spoel]

Matteo Guglielmi wrote:

Hello world,

the following is my input file:


title= 2masn
cpp  = /usr/bin/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 150
init_step= 0
comm_mode= Angular
nstcomm  = 1
comm_grps= Pore
nstxout  = 25
nstvout  = 25
nstfout  = 25
nstcheckpoint= 1000
nstlog   = 2500
nstxtcout= 2500
xtc_grps = System
energygrps   = Pore Membrane Ions Water
nstenergy= 2500
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = Cut-off
rvdw = 1.4
fourier_nx   = 88
fourier_ny   = 88
fourier_nz   = 88
pme_order= 4
ewald_rtol   = 1e-5
ewald_geometry   = 3d
optimize_fft = yes
tcoupl   = berendsen
tc_grps  = Solute Solvent
tau_t= 0.10.4
ref_t= 300300
pcoupl   = berendsen
pcoupltype   = anisotropic
tau_p= 0.5  0.5  0.5  0.50.50.5
compressibility  = 4.53e-5  4.53e-5  4.53e-5  0.00.00.0
ref_p= 1.0251.0251.0251.025  1.025  1.025
gen_vel  = yes
gen_temp = 300
gen_seed = 173529
constraints  = all-bonds
constraint_algorithm = lincs
unconstrained_start  = no
lincs_order  = 4
lincs_iter   = 2
lincs_warnangle  = 30


and way after the very beginning of this simulation (~1.5ns) I always
get this error message:

##
   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.032676  17797  17799   0.003970
After LINCS 0.04  17162  17169   0.00

Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 1434. It should have been within [ 0 .. 1320 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---
#

Is my input file so bad?


I would increase tau_p to at least 5 ps for anisotropic coupling.



(I've seen people using lincs with 5fs time step...)

Thanks for any useful suggestion,
MG.
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] "Range checking error" issue

[Matteo Guglielmi]

Hello world,

the following is my input file:


title= 2masn
cpp  = /usr/bin/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 150
init_step= 0
comm_mode= Angular
nstcomm  = 1
comm_grps= Pore
nstxout  = 25
nstvout  = 25
nstfout  = 25
nstcheckpoint= 1000
nstlog   = 2500
nstxtcout= 2500
xtc_grps = System
energygrps   = Pore Membrane Ions Water
nstenergy= 2500
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = Cut-off
rvdw = 1.4
fourier_nx   = 88
fourier_ny   = 88
fourier_nz   = 88
pme_order= 4
ewald_rtol   = 1e-5
ewald_geometry   = 3d
optimize_fft = yes
tcoupl   = berendsen
tc_grps  = Solute Solvent
tau_t= 0.10.4
ref_t= 300300
pcoupl   = berendsen
pcoupltype   = anisotropic
tau_p= 0.5  0.5  0.5  0.50.50.5
compressibility  = 4.53e-5  4.53e-5  4.53e-5  0.00.00.0
ref_p= 1.0251.0251.0251.025  1.025  1.025
gen_vel  = yes
gen_temp = 300
gen_seed = 173529
constraints  = all-bonds
constraint_algorithm = lincs
unconstrained_start  = no
lincs_order  = 4
lincs_iter   = 2
lincs_warnangle  = 30


and way after the very beginning of this simulation (~1.5ns) I always
get this error message:

##
   Rel. Constraint Deviation:  Maxbetween atoms RMS
   Before LINCS 0.032676  17797  17799   0.003970
After LINCS 0.04  17162  17169   0.00

Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
Grid: 10 x 12 x 12 cells
Grid: 10 x 11 x 12 cells
---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 1434. It should have been within [ 0 .. 1320 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---
#

Is my input file so bad?

(I've seen people using lincs with 5fs time step...)

Thanks for any useful suggestion,
MG.
___
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[gmx-users] Range checking error

[Ibrahim M. Moustafa]

hi gmx-users,

I'm a newbie to gromacs. I have done few mutations to my 
structure and wanted to relax the structure by energy minimization.
  The structure has 8 acetate molecules and 297 water molecules + 
461 protein residues. I generated the
parameters for the acetate using PRODRG server and edited the 
protein.top and protein.gro files (generated with removal of the acetate).

Then running the mdrun
  > mdrun -s em.tpr -c after_em.pdb -g em.log &

  gave me the following error:
"Range checking error" source code file: nsgrid.c: line 226
 Variable ci has a value -2147483648. It should have been within [0 ...4320]
Please report this to the mailing list"

   As explained in the error message, the system might have 
collisions or parameter errors that give particles very high 
velocities ending up with some unrealistic coordinates!


  The em.mdp file looks like:
---
title = 3Dwt_em
cpp   = /usr/bin/cpp ; the c pre-processor
define= -DFLEXIBLE
constraints   = none
integrator= steep ; for steepest decent; cg (for conjugate grad);
nsteps= 5000
nstlist   = 5 ; frequency to update the neighbour list ;
rlist = 0.9
coulombtype   = PME ; use PME to model electrostatic ;
rcoulomb  = 0.9 ; coulomb cutoff distance ;
rvdw  = 1.4 ; radius for LJ or Buckingham potential cutoff ;
fourierspacing= 0.12
fourier_nx= 0
fourier_ny= 0
fourier_nz= 0
pme_order = 4
ewald_rtol= 1e-5
optimize_fft  = yes
;
; Energy minimizing step
;
emtol = 1000.0 ; the minimiz. converges when max force <1000;
emstep= 0.01 ; initial step size = 0.01 nm ;

--

  The question is how to resolve this error so I can do the minimization??

(Any comments on the keywords of the em.mdp file are welcomed)

  many thanks in advance for your help.

  thanks,
 Ibrahim

Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802

Tel  (814) 863 8703
Fax (814) 865 7927

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RE: [gmx-users] range checking error

[Naser, Md Abu]

Hi Giacomo,

That is due to the bad starting structure. You might want to try with small 
time step and with no constrain.

With regards,

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-Original Message-
From: [EMAIL PROTECTED] on behalf of Giacomo Bastianelli
Sent: Tue 05/12/2006 10:16 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] range checking error
 
Dear Users,

I am running MD of an homology model and even with a
long energy minimization step a still get this error message:

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 1200 ]
Please report this to the mailing list (gmx-users@gromacs.org)

Thanks in advance,

Giacomo Bastianelli
___
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[gmx-users] range checking error

[Giacomo Bastianelli]

Dear Users,

I am running MD of an homology model and even with a
long energy minimization step a still get this error message:

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 1200 ]
Please report this to the mailing list (gmx-users@gromacs.org)

Thanks in advance,

Giacomo Bastianelli
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[gmx-users] Range checking error: ci barely out of bounds.

[chris . neale]

I am attempting to solve my range checking errors where ci is just  
barely out of bounds. This particular run is on 4cpus. I have reposted  
because now I have noticed that a0.log differs from the other log  
files with respect to the reported cells in the grid and that this may  
be important. Any help is greatly appreciated.


My error message is:
Variable ci has value 1625. It should have been within [ 0 .. 1584 ]
And I notice that 12 x 12 x 11 = 1584, but 13 x 12 x 11 = 1716 (which  
would put ci=1625 in bounds).


grep 'Grid:' a0.log | wc -l = 24 lines
grep 'Grid:' (a1.log or a2.log or a3.log) | wc -l = 25 lines

The straight grep 'Grid:' output is:
...
Grid: 12 x 12 x 11 cells
Grid: 13 x 12 x 11 cells  (a0.log does not contain this line)

The same pattern tends to occur for different jobs. For another  
example, Grid: 13 x 13 x 10 cells --> Grid: 13 x 13 x 11 cells (not on  
a0.log) and ci = 1721. It should have been within [ 0 .. 1690 ] (But  
13 x 13 x 11 = 1859 putting 1721 in bounds).


Can the grid sizes be different for the different processors or is  
this an output artifact?


Here is my MDP file:
title   =  seriousMD
cpp =  /home/cneale/exe/cpp
integrator  =  md
nsteps  =  35
tinit   =  0
dt  =  0.002
comm_mode   =  linear
nstcomm =  1
comm_grps   =  System
nstxout =  5
nstvout =  5
nstfout =  5
nstlog  =  1000
nstlist =  10
nstenergy   =  5000
nstxtcout   =  5000
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rcoulomb=  0.9
fourierspacing  =  0.12
pme_order   =  4
vdwtype =  cut-off
rvdw_switch =  0
rvdw=  1.4
rlist   =  0.9
DispCorr=  no
Pcoupl  =  Berendsen
pcoupltype  =  semiisotropic
compressibility =  4.5e-5 4.5e-5
ref_p   =  1. 1.
tau_p   =  4.04.0
tcoupl  =  Berendsen
tc_grps =  Protein LDA_POPE_DMPE SOL_NA+
tau_t   =  0.1 0.1   0.1
ref_t   =  300.300.  300.
annealing   =  no
gen_vel =  yes
unconstrained-start =  no
gen_temp=  300.
gen_seed=  9896
constraints =  all-bonds
constraint_algorithm=  lincs
lincs-iter  =  1
lincs-order =  4

There is more background information and run data here:
http://www.gromacs.org/pipermail/gmx-users/2006-October/024154.html
http://www.gromacs.org/pipermail/gmx-users/2006-September/024003.html






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[gmx-users] Range checking error: ci barely out of bounds.

[chris . neale]

Hello, I previously posted a problem about crashes in parallel but not serial:
http://www.gromacs.org/pipermail/gmx-users/2006-September/024003.html
I resolved that problem by running 5ns in serial and then, once I no  
longer needed to restrain the crystal waters, adding them to the main  
TIP4P SOL group.


I then moved my unrestrained simulation to 4cpu parallel and  
everything went fine for 1.5ns when it crashed (see bottom for text  
output upon crash). The energy is stable when viewing output from each  
2ps. So is the pressure based on the .edr and viewing the .xtc, both  
saved every 10ps.


Total Energy: -8e5 +/- 450
Temperature: 300 +/- 1
Pressure(bar): -2 +/- 116
X(nm): 9.2 +/-0.01
Y(nm): 9.1 +/-0.01
Z(nm): 7.7 +/-0.02

This is a protein in a fully solvated membrane with 57K atoms. I am  
running gromacs-3.3.1 in 800ps segments usgin tpbconv -extend to set  
up new runs. I am using shuffle/sort and when I deshuffle the  
trajectory it looks good for the 1.5ns that I have. tau_p=4.0 for  
semiisotropic XY-Z and tau_t=0.1 for each of 3 groups. Constraints are  
all-bonds with lincs and dt=0.002. It may or may not be relevant that  
I have a double [ pairs ] list for my lipids. I have seen people post  
similar neighboursearching issues and received suggestions regarding  
pressure coupling. However, I do not see any obvious pressure issues  
and I am going on strong-but-not-entirely-proven evidence that this is  
a parallel-specific problem.


   Energies (kJ/mol)
  AngleProper Dih. Ryckaert-Bell.  Improper Dih.  LJ-14
4.66383e+041.42350e+041.46400e+041.47575e+032.35022e+04
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coul. recip.
7.84954e+031.04413e+04   -9.08592e+03   -6.09933e+05   -4.18189e+05
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -9.18426e+051.19106e+05   -7.99320e+052.99675e+022.07330e+02

Grid: 13 x 13 x 10 cells
Grid: 13 x 13 x 11 cells
Grid: 13 x 13 x 10 cells
   Step   Time Lambda
 696000 1392.00.0

---
Program mdrun_mpi, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 1721. It should have been within [ 0 .. 1690 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---

"'Nay. We are but men.' Rock!" (Tenacious D)


#

Is it significant that ci was 1721, which is much closer to [ 0 ..  
1690 ] than the -82745956412 type numbers that I get when my system is  
exploding?


Many thanks,
Chris Neale.



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Re: [gmx-users] Range Checking Error

[David van der Spoel]

Gaurav Chopra wrote:

/ />/ />/ />/ Range checking error:
/>/ />/ Explanation: During neighborsearching, we assign each particle 
to a grid
/>/ />/ based on its coordinates. If your system contains collisions or 
parameter
/>/ />/ errors that give particles very high velocities you might end up 
with some
/>/ />/ coordinates being +-Infinity or NaN (not-a-number). Obviously, 
we cannot
/>/ />/ put these on a grid, so this is usually where we detect those 
errors.
/>/ />/ Make sure your system is properly energy-minimized and that the 
potential

/>/ />/ energy seems reasonable before trying again.
/>/ /Please follow the advice in the above two sentences. Check your 
structure.
/>/ />/ I did the energy minimization by increasing the number of steps 
using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
/>/ and steep using -DFLEXIBLE in my mdp file and I was able to compute 
using mdrun but I got the following in my log file

/>/ />/ Initiating Steepest Descents
/>/ Center of mass motion removal mode is Linear
/>/ We have the following groups for center of mass motion removal:
/>/   0:  rest, initial mass: 24594
/>/ Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
/>/ Removing pbc first time
/>/ Done rmpbc
/>/ Steepest Descents:
/>/Tolerance (Fmax)   =  1.0e+01
/>/Number of steps=1
/>/ Grid: 10 x 10 x 20 cells
/>/ Configuring nonbonded kernels...
/>/ Testing AMD 3DNow support... not present.
/>/ Testing ia32 SSE support... present.
/>/ />/ />/ Then with this when I do position restrained md, using 
-DPOSRES in mdp file for grompp and md integrator and then mdrun for 
position restrained

/>/ I get the following
/>/ />/ Step 0, time 0 (ps)  LINCS WARNING
/>/ relative constraint deviation after LINCS:
/>/ max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00

/>/ bonds that rotated more than 30 degrees:
/
turn off the constraints






Hi David

I did turn off the constraints and also made the starting structure 
unconstarined in the mdp file. The mdrun for position restrained gives 
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the 
earlier mail which has to be reviewed by the moderator of gmx list.


Thanks
Gaurav


---
Input Parameters:
  integrator   = md
  nsteps   = 1000
  init_step= 0
  ns_type  = Grid
  nstlist  = 10
  ndelta   = 2
  bDomDecomp   = FALSE
  decomp_dir   = 0
  nstcomm  = 1
  comm_mode= Linear
  nstcheckpoint= 1000
  nstlog   = 1
  nstxout  = 0
  nstvout  = 250
  nstfout  = 0
  nstenergy= 250
  nstxtcout= 250
  init_t   = 0
  delta_t  = 0.002
  xtcprec  = 1000
  nkx  = 42
  nky  = 42
  nkz  = 84
  pme_order= 4
  ewald_rtol   = 1e-05
  ewald_geometry   = 0
  epsilon_surface  = 0
  optimize_fft = FALSE
  ePBC = xyz
  bUncStart= TRUE
  bShakeSOR= FALSE
  etc  = Berendsen
  epc  = Berendsen
  epctype  = Isotropic
  tau_p= 20
  ref_p (3x3):
 ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}
 ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
 ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
  compress (3x3):
 compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
 compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
 compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}
  andersen_seed= 815131
  rlist= 1
  coulombtype  = PME
  rcoulomb_switch  = 0
  rcoulomb = 1
  vdwtype  = Cut-off
  rvdw_switch  = 0
  rvdw = 1
  epsilon_r= 1
  epsilon_rf   = 1
  tabext   = 1
  gb_algorithm = Still
  nstgbradii   = 1
  rgbradii = 2
  gb_saltconc  = 0
  implicit_solvent = No
  DispCorr = No
  fudgeQQ  = 0.5


set this to 1.0 or remove this setting



  free_energy  = no
  init_lambda  = 0
  sc_alpha = 0
  sc_power = 1
  sc_sigma = 0.3
  delta_lambda = 0
  disre_weighting  = Conservative
  disre_mixed  = FALSE
  dr_fc= 1000
  dr_tau   = 0
  nstdisreout  = 100
  orires_fc= 0
  orires_tau   = 0
  nstorireout  = 100
  dihre-fc = 1000
  dihre-tau= 0
  nstdihreout  = 100
  em_stepsize  = 0.01
  em_tol   = 10
  niter= 20
  fc_stepsize  = 0
  nstcgsteep   = 1000
  n

Re: [gmx-users] Range Checking Error

[David van der Spoel]

Gaurav Chopra wrote:

Gaurav Chopra wrote:

/ Hi
/>/ 
/>/ I am doing a steepest descent for the initial mdrun for a peptide and it 
/>/ gives me the following error. Please advice.
/>/ 
/>/ Thanks

/>/ Gaurav
/>/ ---
/>/ Program mdrun, VERSION 3.3
/>/ Source code file: nsgrid.c, line: 226
/>/ 
/>/ Range checking error:

/>/ Explanation: During neighborsearching, we assign each particle to a grid
/>/ based on its coordinates. If your system contains collisions or parameter
/>/ errors that give particles very high velocities you might end up with some
/>/ coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
/>/ put these on a grid, so this is usually where we detect those errors.
/>/ Make sure your system is properly energy-minimized and that the potential
/>/ energy seems reasonable before trying again.
/Please follow the advice in the above two sentences. Check your structure.

I did the energy minimization by increasing the number of steps using steepest 
descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun 
but I got the following in my log file

Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


Then with this when I do position restrained md, using -DPOSRES in mdp file for 
grompp and md integrator and then mdrun for position restrained
I get the following

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00
bonds that rotated more than 30 degrees:


turn off the constraints



also segmentation fault.

Is there a different method to do energy minimization better as suggested in 
the range check error warning.

Thanks
Gaurav



/ 

/>/ Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
/>/ Please report this to the mailing list (gmx-users at gromacs.org 
)
/>/ ---
/>/ 
/>/ ___

/>/ gmx-users mailing listgmx-users at gromacs.org 

/>/ http://www.gromacs.org/mailman/listinfo/gmx-users
/>/ 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/mailing_lists/users.php
/

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
spoel at xray.bmc.uu.se    
spoel at gromacs.org    
http://folding.bmc.uu.se





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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Range Checking Error

[Gaurav Chopra]

/ />/ 
/>/ />/ Range checking error:

/>/ />/ Explanation: During neighborsearching, we assign each particle to a grid
/>/ />/ based on its coordinates. If your system contains collisions or 
parameter
/>/ />/ errors that give particles very high velocities you might end up with 
some
/>/ />/ coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
/>/ />/ put these on a grid, so this is usually where we detect those errors.
/>/ />/ Make sure your system is properly energy-minimized and that the 
potential
/>/ />/ energy seems reasonable before trying again.
/>/ /Please follow the advice in the above two sentences. Check your structure.
/>/ 
/>/ I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE

/>/ and steep using -DFLEXIBLE in my mdp file and I was able to compute using 
mdrun but I got the following in my log file
/>/ 
/>/ Initiating Steepest Descents

/>/ Center of mass motion removal mode is Linear
/>/ We have the following groups for center of mass motion removal:
/>/   0:  rest, initial mass: 24594
/>/ Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
/>/ Removing pbc first time
/>/ Done rmpbc
/>/ Steepest Descents:
/>/Tolerance (Fmax)   =  1.0e+01
/>/Number of steps=1
/>/ Grid: 10 x 10 x 20 cells
/>/ Configuring nonbonded kernels...
/>/ Testing AMD 3DNow support... not present.
/>/ Testing ia32 SSE support... present.
/>/ 
/>/ 
/>/ Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained

/>/ I get the following
/>/ 
/>/ Step 0, time 0 (ps)  LINCS WARNING

/>/ relative constraint deviation after LINCS:
/>/ max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00
/>/ bonds that rotated more than 30 degrees:
/
turn off the constraints






Hi David

I did turn off the constraints and also made the starting structure 
unconstarined in the mdp file. The mdrun for position restrained gives 
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the 
earlier mail which has to be reviewed by the moderator of gmx list.


Thanks
Gaurav


---
Input Parameters:
  integrator   = md
  nsteps   = 1000
  init_step= 0
  ns_type  = Grid
  nstlist  = 10
  ndelta   = 2
  bDomDecomp   = FALSE
  decomp_dir   = 0
  nstcomm  = 1
  comm_mode= Linear
  nstcheckpoint= 1000
  nstlog   = 1
  nstxout  = 0
  nstvout  = 250
  nstfout  = 0
  nstenergy= 250
  nstxtcout= 250
  init_t   = 0
  delta_t  = 0.002
  xtcprec  = 1000
  nkx  = 42
  nky  = 42
  nkz  = 84
  pme_order= 4
  ewald_rtol   = 1e-05
  ewald_geometry   = 0
  epsilon_surface  = 0
  optimize_fft = FALSE
  ePBC = xyz
  bUncStart= TRUE
  bShakeSOR= FALSE
  etc  = Berendsen
  epc  = Berendsen
  epctype  = Isotropic
  tau_p= 20
  ref_p (3x3):
 ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}
 ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
 ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
  compress (3x3):
 compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
 compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
 compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}
  andersen_seed= 815131
  rlist= 1
  coulombtype  = PME
  rcoulomb_switch  = 0
  rcoulomb = 1
  vdwtype  = Cut-off
  rvdw_switch  = 0
  rvdw = 1
  epsilon_r= 1
  epsilon_rf   = 1
  tabext   = 1
  gb_algorithm = Still
  nstgbradii   = 1
  rgbradii = 2
  gb_saltconc  = 0
  implicit_solvent = No
  DispCorr = No
  fudgeQQ  = 0.5
  free_energy  = no
  init_lambda  = 0
  sc_alpha = 0
  sc_power = 1
  sc_sigma = 0.3
  delta_lambda = 0
  disre_weighting  = Conservative
  disre_mixed  = FALSE
  dr_fc= 1000
  dr_tau   = 0
  nstdisreout  = 100
  orires_fc= 0
  orires_tau   = 0
  nstorireout  = 100
  dihre-fc = 1000
  dihre-tau= 0
  nstdihreout  = 100
  em_stepsize  = 0.01
  em_tol   = 10
  niter= 20
  fc_stepsize  = 0
  nstcgsteep   = 1000
  nbfgscorr= 10
  ConstAlg = Lincs
  shake_tol

[gmx-users] Range Checking Error

[Gaurav Chopra]

 />/ 
> />/ Range checking error:
> />/ Explanation: During neighborsearching, we assign each particle to a grid
> />/ based on its coordinates. If your system contains collisions or parameter
> />/ errors that give particles very high velocities you might end up with some
> />/ coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> />/ put these on a grid, so this is usually where we detect those errors.
> />/ Make sure your system is properly energy-minimized and that the potential
> />/ energy seems reasonable before trying again.
> /Please follow the advice in the above two sentences. Check your structure.
> 
> I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
> and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
> 
> Initiating Steepest Descents
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  rest, initial mass: 24594
> Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
> Removing pbc first time
> Done rmpbc
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+01
>Number of steps=1
> Grid: 10 x 10 x 20 cells
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
> 
> 
> Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
> I get the following
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
> bonds that rotated more than 30 degrees:

turn off the constraints

>

Hi David

I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.

Thanks
Gaurav


---
Input Parameters:
   integrator   = md
   nsteps   = 1000
   init_step    = 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   bDomDecomp   = FALSE
   decomp_dir   = 0
   nstcomm  = 1
   comm_mode    = Linear
   nstcheckpoint    = 1000
   nstlog   = 1
   nstxout  = 0
   nstvout  = 250
   nstfout  = 0
   nstenergy    = 250
   nstxtcout    = 250
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 42
   nky  = 42
   nkz  = 84
   pme_order    = 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bUncStart    = TRUE
   bShakeSOR    = FALSE
   etc  = Berendsen
   epc  = Berendsen
   epctype  = Isotropic
   tau_p    = 20
   ref_p (3x3):
  ref_p[    0]={ 1.0e+00,  0.0e+00,  0.0e+00}
  ref_p[    1]={ 0.0e+00,  1.0e+00,  0.0e+00}
  ref_p[    2]={ 0.0e+00,  0.0e+00,  1.0e+00}
   compress (3x3):
  compress[    0]={ 4.5e-05,  0.0e+00,  0.0e+00}
  compress[    1]={ 0.0e+00,  4.5e-05,  0.0e+00}
  compress[    2]={ 0.0e+00,  0.0e+00,  4.5e-05}
   andersen_seed    = 815131
   rlist    = 1
   coulombtype  = PME
   rcoulomb_switch  = 0
   rcoulomb = 1
   vdwtype  = Cut-off
   rvdw_switch  = 0
   rvdw = 1
   epsilon_r    = 1
   epsilon_rf   = 1
   tabext   = 1
   gb_algorithm = Still
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   implicit_solvent = No
   DispCorr = No
   fudgeQQ  = 0.5
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 1
   sc_sigma = 0.3
   delta_lambda = 0
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc    = 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc    = 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   dihre-tau    = 0
   nstdihreout  = 100
   em_stepsize  = 0.01
   em_tol   = 10
   niter    = 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr    = 10
   ConstAlg = Lincs
   shake_tol

[gmx-users] Range Checking error

[Gaurav Chopra]

Gaurav Chopra wrote:

/ Hi
/>/ 
/>/ I am doing a steepest descent for the initial mdrun for a peptide and it 
/>/ gives me the following error. Please advice.
/>/ 
/>/ Thanks

/>/ Gaurav
/>/ ---
/>/ Program mdrun, VERSION 3.3
/>/ Source code file: nsgrid.c, line: 226
/>/ 
/>/ Range checking error:

/>/ Explanation: During neighborsearching, we assign each particle to a grid
/>/ based on its coordinates. If your system contains collisions or parameter
/>/ errors that give particles very high velocities you might end up with some
/>/ coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
/>/ put these on a grid, so this is usually where we detect those errors.
/>/ Make sure your system is properly energy-minimized and that the potential
/>/ energy seems reasonable before trying again.
/Please follow the advice in the above two sentences. Check your structure.

I did the energy minimization by increasing the number of steps using steepest 
descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun 
but I got the following in my log file

Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
 0:  rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
  Tolerance (Fmax)   =  1.0e+01
  Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


Then with this when I do position restrained md, using -DPOSRES in mdp file for 
grompp and md integrator and then mdrun for position restrained
I get the following

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 
40665803128832.00
bonds that rotated more than 30 degrees:

also segmentation fault.

Is there a different method to do energy minimization better as suggested in 
the range check error warning.

Thanks
Gaurav



/ 

/>/ Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
/>/ Please report this to the mailing list (gmx-users at gromacs.org 
)
/>/ ---
/>/ 
/>/ ___

/>/ gmx-users mailing listgmx-users at gromacs.org 

/>/ http://www.gromacs.org/mailman/listinfo/gmx-users
/>/ 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/mailing_lists/users.php
/

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
spoel at xray.bmc.uu.se    
spoel at gromacs.org    
http://folding.bmc.uu.se


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[gmx-users] Range Checking Error

[Gaurav Chopra]

Gaurav Chopra wrote:
> Hi
> 
> I am doing a steepest descent for the initial mdrun for a peptide and it 
> gives me the following error. Please advice.
> 
> Thanks
> Gaurav
> ---
> Program mdrun, VERSION 3.3
> Source code file: nsgrid.c, line: 226
> 
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
Please follow the advice in the above two sentences. Check your structure.

I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file

Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
I get the following

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
bonds that rotated more than 30 degrees:

also segmentation fault.

Is there a different method to do energy minimization better as suggested in the range check error warning.

Thanks
Gaurav



> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> ---
> 
> ___
> gmx-users mailing listgmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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/mailing_lists/users.php


-- 
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se



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Re: [gmx-users] Range checking error

[David van der Spoel]

Gaurav Chopra wrote:

Hi

I am doing a steepest descent for the initial mdrun for a peptide and it 
gives me the following error. Please advice.


Thanks
Gaurav
---
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Please follow the advice in the above two sentences. Check your structure.



Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---

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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Range checking error

[Gaurav Chopra]

Hi

I am doing a steepest descent for the initial mdrun for a peptide and it 
gives me the following error. Please advice.


Thanks
Gaurav
---
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---

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