From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Sun Sep 08 2013 - 01:02:31 CDT
Hi James,
CHARMM-GUI membrane builder can sometimes place acyl chains through rings
contained in aromatic residues, cholesterol, etc. Have you checked for
this, if you have cholesterol in your system? It is a possible source of
RATTLE errors.
cheers,
Grace
On Sun, Sep 8, 2013 at 12:56 AM, James Starlight <jmsstarlight_at_gmail.com>wrote:
> Emilia,
>
> I've already tried to increase minimization step number but result was the
> same.
>
> Briefly I've just tried to minimize my system (for example the system
> which I've shown or also I have the same system with reduced water layers)
> during equilibration step6.1 with namd 2.9(gpu-simulation regime). By the
> way what other options of the minimization can I change besides step number
> as well as integrator timestep (e.g can I vary gradient degree or
> minimization algorithm )?
>
> James
>
>
> 2013/9/7 Emilia Wu <emilia.l.wu_at_gmail.com>
>
>> You can minimize more steps before dynamics starts. The default number in
>> the input might be too small for your big system.
>>
>> Emilia
>>
>> On Sep 7, 2013, at 4:04 AM, James Starlight wrote:
>>
>> Emillia,
>>
>> I've tried to launch simulation from the files produced by charm-gui but
>> simulation have crashed on the beginning of the first equilibration step
>> after long minimization with the error
>>
>> TCL: Original numsteps 90000000 will be ignored.
>> TCL: Running for 25000 steps
>> REASSIGNING VELOCITIES AT STEP 0 TO 303.15 KELVIN.
>> Pe 2 has 36 local and 36 remote patches and 972 local and 972 remote
>> computes.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4962!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 5678!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 2288!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 5370!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3089!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3759!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 20746!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 14993!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 2681!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4697!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1669!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1634!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4731!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 2191!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 6835!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 942!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 11615!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3217!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 7862!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1920!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 723!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1030!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 2733!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 262!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 336!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1259!
>> ERROR: Constraint failure in RATTLE algorithm for atom 1201!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3491!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 5287!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 145!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 6863!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 7462!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1811!
>> ERROR: Constraint failure in RATTLE algorithm for atom 397!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 854!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1453!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1792!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 8914!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 10618!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3135!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 7368!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 13152!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 6171!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 8533!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 21871!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 9658!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1715!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 2824!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 12533!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 8990!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 751!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4164!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 6875!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 175!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1156!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 455!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 9569!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 1535!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 435!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 7012!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 5552!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3525!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3266!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 256!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 6265!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 3155!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 2209!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 24!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4392!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4495!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 4751!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Constraint failure in RATTLE algorithm for atom 552!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Exiting prematurely; see error messages above.
>>
>>
>> It looks like my system have not been equilibrated properly and I have
>> the same eror only in case of big systems. How I could fix it?
>>
>> James
>>
>>
>>
>> 2013/9/7 Sunhwan Jo <sunhwan_at_uchicago.edu>
>>
>>> James,
>>>
>>> My labmate has downloaded your files and ran step6.1 input
>>> using NAMD_2.9_Linux-x86_64-TCP/namd2. We didn't find any problems with the
>>> minimization and it was working well in our test.
>>>
>>> Sunhwan
>>>
>>> On Sep 6, 2013, at 11:24 AM, James Starlight <jmsstarlight_at_gmail.com>
>>> wrote:
>>>
>>> Dear all !
>>>
>>> Thanks for suggestions!
>>>
>>> I've mentioned in the adjacent topic the problem of minimization for
>>> the system consisted of many lipids + water (produced by charm_gui).
>>>
>>> Briefly when I try to minimize clashes in big systems ( many lipids +
>>> solvent) the minimization didt work ( its looks like all atoms were frozen
>>> during whole minimization trajectory so the clashes didnt resolved ).
>>>
>>> When I try to minimize the same system without water (only lipids)-
>>> there were no problem at all (the lipid tales constantly moves during
>>> minimization resolving clashes between them) .
>>>
>>> To fix this problem I've tried to add FIX ATOMS to all water according
>>> to tutorial but the problem have not been solved in case of big systems.
>>> How I should minimize it ?
>>>
>>>
>>> 2013/9/6 Sunhwan Jo <sunhwan_at_uchicago.edu>
>>>
>>>> James
>>>>
>>>> CHARMM-GUI generates step_assembly.xplor.psf, which can be used in
>>>> NAMD. Perhaps this file is not displayed on webpage. You can download every
>>>> file generated by GUI by using "download .tgz" link on the upper right
>>>> corner of the webpage.
>>>>
>>>> Sunhwan
>>>>
>>>> Sent from my iPhone
>>>>
>>>> On Sep 6, 2013, at 6:35 AM, "James Starlight" <jmsstarlight_at_gmail.com>
>>>> wrote:
>>>>
>>>> Dear Namd Users!
>>>>
>>>> I've already seen similar topic previously but didn't find any
>>>> possible solution.
>>>>
>>>> How I could use charm gui outputs to generate namd psf file of the
>>>> generated membrane ? In my case charm gui generated 6 files
>>>>
>>>> http://www.charmm-gui.org/?doc=input/membrane_only&time=1378378701
>>>>
>>>>
>>>> Equilibration Step1: step6.1_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.1_equilibration.inp> Equilibration
>>>> Step2: step6.2_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.2_equilibration.inp> Equilibration
>>>> Step3: step6.3_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.3_equilibration.inp> Equilibration
>>>> Step4: step6.4_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.4_equilibration.inp> Equilibration
>>>> Step5: step6.5_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.5_equilibration.inp> Equilibration
>>>> Step6: step6.6_equilibration.inp<http://www.charmm-gui.org/uploaded_pdb/1378378701/step6.6_equilibration.inp>
>>>> but how I can create psf from that data?
>>>>
>>>>
>>>> James
>>>>
>>>>
>>>
>>>
>>
>>
>
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