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

[Itamar Kass]

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:
>>>>>> 
>>>>> --
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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
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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
> 
> ========================================
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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
============================================