[gmx-users] GROMACS 4.5.4 keep crashing all the time

Thu Sep 1 07:43:22 CEST 2011

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.neale at 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
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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.
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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
>>> ============================================
>> 
>> -- 
>> ========================================
>> 
>> 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
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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
============================================