Hi Itamar,

I haven't really followed the discussion and I'm a bit too lazy to
look it all up now ;) But have you tried setting the nst parameters to
1  (except for output). Especially nstpcouple. Note that nstpcouple=1
requires nstlist=1 and nstcalcenergy=1. If that solves the problem,
you may need to extend your equilibration a bit, first relaxing NVT,
followed by NPT with nstpcouple=1, thereafter equilibrating using
productions conditions. It it solves it, maybe the option should be
renamed nstptrouble :p

Hope it helps,

Tsjerk

On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass <itamar.k...@monash.edu> wrote:
> 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!
>>>>>>> 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
>>>>>> ============================================
>>>>>>
>>>>> --
>>>>> 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
>>>
>>> ========================================
>>> --
>>> 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
>>
>>
>> --
>> 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
> ============================================
>
> --
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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