Re: [gmx-users] Problem in equilibration for membrane system

2009-10-07 Thread Itamar Kass 
hi Bing,

I advice you to look carefully on any clashes between POPC and the
protein. It might happen that one lipid was 'trapped' inside the
protein or more likely that atom water had trapped and that what crash
you system.

Cheers,
Itamar

---

 "In theory, there is no difference between theory and practice. But,
in practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au


On Wed, Oct 7, 2009 at 9:47 PM, Justin A. Lemkul  wrote:
>
>
> Bing Bing wrote:
>>
>> My protein complex was minimized initially before putting into the lipid.
>> POPC is also a preequilibrated structure from Tielemen website. I don't
>> quite understand on what you meant by "the protein is not happy with the
>> restraint". The system went well through out the nvt, npt with
>
> I think what Mark was getting as was if you're restraining some unusual or
> inappropriate geometry, you can get nasty results when you turn off
> restraints.  I don't know that this is the case in your situation.
>
>> restraint on protein Once it move to md production run ( which is
>> without restraint on protein), error occurred (range checking error). The
>> reason i'm using the version3.3.2 is because the forcefield i'm using at the
>> moment only support version3.3.2.  Is my problem cause by
>
> I don't understand this statement.  The force field you mentioned is most
> certainly supported in the newest version of Gromacs, in fact my tutorial
> was written for the version 4.0.x series.  Please also see the advanced
> troubleshooting page I provide; you may find some ideas there.
>
> Certainly, watch the trajectory and see where things are going wrong to
> deduce the nature of the issue.
>
> -Justin
>
>> bug of the older version? is there any bugfix fot this? please
>> help.
>>
>> regards,
>> Bing
>>
>>
>> On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham > > wrote:
>>
>>    Bing Bing wrote:
>>
>>        Dear All,
>>        I'm running the protein complex with POPC system. NVT (100ps)
>>        and NPT (200ps) were done with restraint on the protein follow
>>        by 1000 ps of NPT without restraint on protein. The trajectory
>>        was checked in term of pressure, potential, area per lipid
>>        were checked and everything seems ok (potential almost
>>        plateu, area per lipid close to experimental value). I proceeded
>>        with md (similar to Justin's tutorial) for 1 ns. The simulation
>>        stop around 800ps with the range checking error.
>>
>>
>>    OK so look at the collective variables, and/or trajectory to find
>>    evidence of the problem. The most likely explanation is that your
>>    protein was unhappy in the restraints, of course. Perhaps you should
>>    try some vacuum EM before you embed it in the lipid, or some such.
>>
>>
>>        I'm using gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired
>>        to be more gentle while releasing the restraint.Different
>>        stepwise of releasing the restraint during NPT were tried and
>>        followed by production MD, all the simulation stop or i shall
>>        said it crashed around ~800ps with the same error (range
>>        checking error). I'm out of idea what is the problem here.
>>        Please advice.
>>
>>
>>    Range checking is just one of many things that can be the first
>>    thing to break when there's an underlying systemic problem.
>>
>>    Also, unless you need scientific continuity, 3.3.2 is about 4 years
>>    old... 4.0.5 will be much faster!
>>
>>    Mark
>>    ___
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>>    
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at http://www.gromacs.org/search before
>>    posting!
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>>    interface or send it to gmx-users-requ...@gromacs.org
>>    .
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>>
>>
>>
>> 
>>
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>
> --
> 
>
> Just

Re: [gmx-users] Problem in equilibration for membrane system

2009-10-07 Thread Justin A. Lemkul 



Bing Bing wrote:
My protein complex was minimized initially before putting into the 
lipid. POPC is also a preequilibrated structure from Tielemen website. I 
don't quite understand on what you meant by "the protein is not happy 
with the restraint". The system went well through out the nvt, npt with 


I think what Mark was getting as was if you're restraining some unusual or 
inappropriate geometry, you can get nasty results when you turn off restraints. 
 I don't know that this is the case in your situation.


restraint on protein Once it move to md production run ( which is 
without restraint on protein), error occurred (range checking error). 
The reason i'm using the version3.3.2 is because the forcefield i'm 
using at the moment only support version3.3.2.  Is my problem cause by 


I don't understand this statement.  The force field you mentioned is most 
certainly supported in the newest version of Gromacs, in fact my tutorial was 
written for the version 4.0.x series.  Please also see the advanced 
troubleshooting page I provide; you may find some ideas there.


Certainly, watch the trajectory and see where things are going wrong to deduce 
the nature of the issue.


-Justin


bug of the older version? is there any bugfix fot this? please
help.

regards,
Bing


On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham > wrote:


Bing Bing wrote:

Dear All,
I'm running the protein complex with POPC system. NVT (100ps)
and NPT (200ps) were done with restraint on the protein follow
by 1000 ps of NPT without restraint on protein. The trajectory
was checked in term of pressure, potential, area per lipid
were checked and everything seems ok (potential almost
plateu, area per lipid close to experimental value). I proceeded
with md (similar to Justin's tutorial) for 1 ns. The simulation
stop around 800ps with the range checking error.


OK so look at the collective variables, and/or trajectory to find
evidence of the problem. The most likely explanation is that your
protein was unhappy in the restraints, of course. Perhaps you should
try some vacuum EM before you embed it in the lipid, or some such.


I'm using gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired
to be more gentle while releasing the restraint.Different
stepwise of releasing the restraint during NPT were tried and
followed by production MD, all the simulation stop or i shall
said it crashed around ~800ps with the same error (range
checking error). I'm out of idea what is the problem here.
Please advice.


Range checking is just one of many things that can be the first
thing to break when there's an underlying systemic problem.

Also, unless you need scientific continuity, 3.3.2 is about 4 years
old... 4.0.5 will be much faster!

Mark
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--


Justin A. Lemkul
Ph.D. Candidate
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] Problem in equilibration for membrane system

2009-10-07 Thread Bing Bing 
My protein complex was minimized initially before putting into the lipid.
POPC is also a preequilibrated structure from Tielemen website. I don't
quite understand on what you meant by "the protein is not happy with the
restraint". The system went well through out the nvt, npt with restraint on
protein Once it move to md production run ( which is without restraint
on protein), error occurred (range checking error).
The reason i'm using the version3.3.2 is because the forcefield i'm using at
the moment only support version3.3.2.  Is my problem cause by bug of the
older version? is there any bugfix fot this? please
help.

regards,
Bing


On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham wrote:

> Bing Bing wrote:
>
>> Dear All,
>> I'm running the protein complex with POPC system. NVT (100ps) and NPT
>> (200ps) were done with restraint on the protein follow by 1000 ps of NPT
>> without restraint on protein. The trajectory was checked in term of
>> pressure, potential, area per lipid were checked and everything seems ok
>> (potential almost plateu, area per lipid close to experimental value). I
>> proceeded with md (similar to Justin's tutorial) for 1 ns. The simulation
>> stop around 800ps with the range checking error.
>>
>
> OK so look at the collective variables, and/or trajectory to find evidence
> of the problem. The most likely explanation is that your protein was unhappy
> in the restraints, of course. Perhaps you should try some vacuum EM before
> you embed it in the lipid, or some such.
>
>  I'm using gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired to be more
>> gentle while releasing the restraint.Different stepwise of releasing the
>> restraint during NPT were tried and followed by production MD, all the
>> simulation stop or i shall said it crashed around ~800ps with the same error
>> (range checking error). I'm out of idea what is the problem here. Please
>> advice.
>>
>
> Range checking is just one of many things that can be the first thing to
> break when there's an underlying systemic problem.
>
> Also, unless you need scientific continuity, 3.3.2 is about 4 years old...
> 4.0.5 will be much faster!
>
> Mark
> ___
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> Please search the archive at http://www.gromacs.org/search before posting!
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>
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Re: [gmx-users] Problem in equilibration for membrane system

2009-10-07 Thread Mark Abraham 

Bing Bing wrote:

Dear All,
I'm running the protein complex with POPC system. NVT (100ps) and NPT 
(200ps) were done with restraint on the protein follow by 1000 ps of NPT 
without restraint on protein. The trajectory was checked in term of 
pressure, potential, area per lipid were checked and everything 
seems ok (potential almost plateu, area per lipid close to experimental 
value). I proceeded with md (similar to Justin's tutorial) for 1 ns. The 
simulation stop around 800ps with the range checking error.


OK so look at the collective variables, and/or trajectory to find 
evidence of the problem. The most likely explanation is that your 
protein was unhappy in the restraints, of course. Perhaps you should try 
some vacuum EM before you embed it in the lipid, or some such.


I'm using 
gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired to be more gentle 
while releasing the restraint.Different stepwise of releasing the 
restraint during NPT were tried and followed by production MD, all the 
simulation stop or i shall said it crashed around ~800ps with the same 
error (range checking error). I'm out of idea what is the problem here. 
Please advice.


Range checking is just one of many things that can be the first thing to 
break when there's an underlying systemic problem.


Also, unless you need scientific continuity, 3.3.2 is about 4 years 
old... 4.0.5 will be much faster!


Mark
___
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