Re: Constraint failure in RATTLE algorithm for atom 6!

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Tue Apr 26 2016 - 16:46:40 CDT

Dear Brian,

I used the CHARMM General FF. I just used some abbreviations for simplicity.

So, what is your suggestion?

Regards,
Farideh

On Wed, Apr 27, 2016 at 2:10 AM, Radak, Brian K <bradak_at_anl.gov> wrote:

> Other than a slight distortion from nonlinearity in that alkyne, there
> doesn't seem to be anything too wrong with your structure.
>
> What parameters are you using? I don't see the CGT1 and CGT2 types
> anywhere in the CHARMM force field.
>
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
> ------------------------------
> *From:* faride badalkhani [farideh.khamseh_at_gmail.com]
> *Sent:* Tuesday, April 26, 2016 4:31 PM
> *To:* Radak, Brian K
> *Cc:* namd-l_at_ks.uiuc.edu; jeffcomer_at_gmail.com
>
> *Subject:* Re: namd-l: Constraint failure in RATTLE algorithm for atom 6!
>
> I used the tcl command to construct the PSF.
> the attached file is pdb and psf and the command I used to construct psf.
>
> Regards,
> Farideh
>
>
> On Tue, Apr 26, 2016 at 5:26 PM, Radak, Brian K <bradak_at_anl.gov> wrote:
>
>> How did you construct the PSF? Was it with psfgen and/or VMD? Can you
>> post an input script with the *exact* commands that you used?
>>
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
>> brian.radak_at_anl.gov
>> ------------------------------
>> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
>> faride badalkhani [farideh.khamseh_at_gmail.com]
>> *Sent:* Tuesday, April 26, 2016 4:22 PM
>> *To:* namd-l; jeffcomer_at_gmail.com
>> *Subject:* Re: namd-l: Constraint failure in RATTLE algorithm for atom 6!
>>
>> Hi,
>>
>> It is an internal alkyne carbon!
>> H
>> |
>> H---C==*C*---C---O---H
>> |
>> H
>>
>> Regards,
>> Farideh
>>
>> On Wed, Apr 27, 2016 at 1:47 AM, faride badalkhani <
>> farideh.khamseh_at_gmail.com> wrote:
>>
>>> Thanks for your answer and time.
>>>
>>> Regards,
>>> Farideh
>>>
>>> On Tue, Apr 26, 2016 at 7:44 PM, Arash Azari <arashazari.temp_at_gmail.com>
>>> wrote:
>>>
>>>> salam Farideh,
>>>>
>>>> I am not expert in this field, but I think this question has been
>>>> answered in the mailing-list.
>>>> Based on my previous experience, it simply indicates that the system
>>>> did not well minimized before running the simulation. You need much longer
>>>> minimization.
>>>> As I remember from your previous emails, you used 0.5 fs time step
>>>> which is not the step which normally people use in their MD simulations;
>>>> you should use something around 2 fs. Please have a look at user manual.
>>>> Please repeat everything with this time step and minimize the system
>>>> much longer; it depends on the size of your system and the number of atoms.
>>>> You should perform: minimization, (gradual heating depending on what
>>>> you have done and need) equilibration, and main simulation. In some cases
>>>> it is recommended to minimize the system a couple of times followed by
>>>> equilibration.
>>>> I hope this helps.
>>>> One more thing; please do not post too much question to the mailing
>>>> list as people will ignore very frequent questions.
>>>> Probably you can get much better help from your colleagues at your
>>>> research group (Department).
>>>> Please let me know if you solve the problem.
>>>> Good luck!
>>>>
>>>>
>>>> Best regards,
>>>> Arash
>>>>
>>>> On Mon, Apr 25, 2016 at 5:42 PM, faride badalkhani <
>>>> farideh.khamseh_at_gmail.com> wrote:
>>>>
>>>>> Dear NAMD users,
>>>>>
>>>>> I am trying to simulate a hyperbranched polymer in a water box. I
>>>>> defined the patches and built the Protein Structure File (PSF) using a tcl
>>>>> command, and there was nothing strange in psf file format. when I run a NVT
>>>>> simulation for 500 ps I got this error message:
>>>>>
>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 6!
>>>>> ERROR: Constraint failure; simulation has become unstable.
>>>>> ERROR: Exiting prematurely; see error messages above.
>>>>>
>>>>> So, I reviewed NAMD mailing list and checked periodic cell size. I had
>>>>> minimized the system for 25 ps. I tried looking at my psf and pdb files in
>>>>> VMD. There was no atom with (0, 0, 0) coordinates.
>>>>> I set the MARGIN parameter to 5 in the NAMD configuration file.
>>>>>
>>>>> But I got the same error. Therefore, I tried the simulated annealing
>>>>> in vacuum. But, it does not work, too.
>>>>>
>>>>> Atom 6 (in fact, 5) is an internal alkyne carbon! and the residue has
>>>>> a shape of
>>>>>
>>>>> RESI POC -0.235 !
>>>>> GROUP
>>>>> ATOM HA H 0.421
>>>>> ATOM O1 OH1 -0.899 !
>>>>> ATOM C1 CT2 0.198 ! H1
>>>>> ATOM H1 HA2 0.090 ! __ |
>>>>> ATOM H2 HA2 0.090 ! H3--C3==C2--C1--O1--HA
>>>>> ATOM C2 CGT1 -0.015 ! |
>>>>> ATOM C3 CGT2 -0.410 ! H2
>>>>> ATOM H3 HGP 0.290 !
>>>>> BOND H3 C3 C3 C2 C2 C1 C1 O1
>>>>> BOND C1 H1 C1 H2 O1 HA
>>>>> DONOR O1 HA
>>>>> ACCEPTOR O1
>>>>> PATCHING FIRS NONE LAST NONE
>>>>>
>>>>> Any help will be appreciated.
>>>>>
>>>>> Regards,
>>>>> Farideh
>>>>>
>>>>
>>>>
>>>
>>
>

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