HI Chris,

I am sorry that from my mails it is seems like I am not appreciate the help, 
because I appreciate it much. It is just the fact that I am trying to give as 
much info as I can and to go over any idea in the mailing list without actually 
delay my other stuff. So again, I wish thanks for anyone who is helps here.

 
On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote:

> Itamar:
> 
> We really are trying to help. I think that perhaps you don't grasp how 
> difficult it is to help without being able to access the simulation directly. 
> Therefore we have ideas and we ask you to do specific things that are going 
> to move us toward a solution, either by finding answers or by ruling out 
> possibilities.
> 
> It is actually useful information to know that "Sometimes it is the peptide N 
> and H, like in the case of 981 and 982, and sometimes others" ... but when it 
> seems like you don't want to provide the requested information my first 
> inclination is to give up on trying to help.
> 
> At this point, there are a few unanswered old questions and I have some new 
> questions.
> 
> 1. Can you reproduce this with a water box?

The error is reproducible in a box of protein and water only.

> 2. Can you reproduce this with your protein in vacuum?

The error is reproduced in vacuum.

> 3. If neither 2 or 3, then can you step slowly from one of these systems 
> toward your final system and identify the point at which the lincs warnings 
> arise?
> 4. Do you get the warnings without Ca also, or just with Ca?

I am not sure what this mean. I get this warning mainly for N-H, but also for 
Ca-C, pairs of atoms 

> 5. Can you reproduce this with the SD integrator? If you are really against 
> trying this, then at least can you reproduce this with a single Berendsen 
> temperature coupling group?

When I use SD integrator, the simulations run fine.

> 6. Can you reproduce this without using the reaction field? Either with PME 
> or a simple cutoff?

Using PME the system is running just fine.

> 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where 
> you start to see this warning?

I can't tell, 'cause I jump from 4.0.7 to 4.5.4.

Thanks for the help,
Itamar

> 
> Chris.
> 
> -- original message --
> 
> Hi Justin,
> 
> I did repeat it using gen_val and running temperature the same, with no 
> effect, it is still crash. I didn't replied point #6 because the atoms which 
> triggers the LINCS are different between each try. Sometimes it is the 
> peptide N and H, like in the case of 981 and 982, and sometimes others. In 
> addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 
> I can find.
> 
> Itamar
> 
> 
> On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote:
> 
>> 
>> 
>> Itamar Kass wrote:
>>> Hi Mark,
>>> I didn't had the time to do the SD yet, but serial run end with the same 
>>> results. I didn't try water only system, as this is of no interest to me, 
>>> but I will simplify the system later on.
>> 
>> Being of interest to you and being a useful diagnostic may be different.  
>> It's important to rule out different variables to arrive at a solution, 
>> which I suspect is of interest to you.  You also haven't addressed points #1 
>> and #6 in Chris' message.
>> 
>> -Justin
>> 
>>> Cheers,
>>> Itamar
>>> On 01/09/2011, at 10:51 AM, Mark Abraham wrote:
>>>> On 1/09/2011 10:20 AM, Itamar Kass wrote:
>>>>> Hi Chris,
>>>>> 
>>>>> Thanks for the email, I am sorry it took me some time to replay. I tried 
>>>>> 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and 
>>>>> again the simulations had stopped after 1000 LINCS error (I can extend 
>>>>> the simulations using 4.0.7).
>>>>> 
>>>>> I know that gromacs stopped after 1000 LINCS, but this is usually a sign 
>>>>> that something bad is going on in the system.
>>>> OK. Chris suggested a number of other strategies that will help determine 
>>>> which aspect of 4.5.4 is behaving differently. How did those strategies 
>>>> work out?
>>>> 
>>>> Mark
>>>> 
>>>>> Cheers,
>>>>> Itamar
>>>>> 
>>>>> On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote:
>>>>> 
>>>>>> OK, here's my last few ideas:
>>>>>> 
>>>>>> 1. Please try to repeat this with gen_vel set to the same value as your 
>>>>>> temperature coupling
>>>>>> 
>>>>>> 2. Can you reproduce this in serial?
>>>>>> 
>>>>>> 3. Can you reproduce this with the sd integrator?
>>>>>> 
>>>>>> 4. Can you reproduce this with a simpler system? protein in vacuum or 
>>>>>> just water or remove the ions, etc?
>>>>>> 
>>>>>> 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it 
>>>>>> under 4.5.4. Do you get the same lincs warnings?
>>>>>> 
>>>>>> 6. Also, note that you are getting warnings and the run does not 
>>>>>> actually crash but just stops after too many warnings. So what are atoms 
>>>>>> 981 and 982? Does their motion look different in an important ways 
>>>>>> between the 4.0.7 and 4.5.4 trajectories?
>>>>>> 
>>>>>> Chris.
>>>>>> 
>>>>>> -- original message --
>>>>>> 
>>>>>> Hi Chris,
>>>>>> 
>>>>>> thanks for the advice, I have to say I tried this as well without any 
>>>>>> success.
>>>>>> 
>>>>>> Itamar
>>>>>> 
>>>>>> On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:
>>>>>> 
>>>>>>> run an EM with flexible water. I often find that this is the only way 
>>>>>>> to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or 
>>>>>>> different depending on your water model I think) should be enough.
>>>>>>> 
>>>>>>> Chris.
>>>>>>> 
>>>>>>> Hi Chris and Justin,
>>>>>>> 
>>>>>>> On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
>>>>>>> 
>>>>>> --
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at 
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>> -----
>>>>> "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.Kass at monash.edu
>>>>> ============================================
>>>>> 
>>>> -- 
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at 
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> -----
>>> "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.Kass at monash.edu
>>> ============================================
>> 
>> -- 
>> ========================================
>> 
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
>> ========================================
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>> gmx-users mailing list    gmx-users at gromacs.org
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -----
> "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.Kass at monash.edu
> 
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-----
"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...@monash.edu
============================================

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