Re: NVT and NPT simulationd

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Wed Dec 14 2016 - 12:14:08 CST

Dear Prof. Geist,

I do not have any fixed atoms in my structure, but as you can find in the
.pdb and .psf files below the residue number 0 (POC) includes an alkyne
group and I got the parameters from the CHARMM 36 FF and CHARMM General FF.
Thank you for chacking the structure. you can find the .pdb and .psf files
in the link below:

<https://www.dropbox.com/sh/y8wgl56qdw1ez9s/AADUtuIxeoIve4Q7K8uSyW7oa?dl=0>
https://www.dropbox.com/sh/y8wgl56qdw1ez9s/AADUtuIxeoIve4Q7K8uSyW7oa?dl=0

Regards,
Farideh

On Wed, Dec 14, 2016 at 8:39 PM, faride badalkhani <
farideh.khamseh_at_gmail.com> wrote:

> Dear Prof. Geist,
>
> I do not have any fixed atoms in my structure, but as you can find in the
> .pdb and .psf files below the residue number 0 (POC) includes an alkyne
> group and I got the parameters from the CHARMM 36 FF and CHARMM General FF.
> Thank you for chacking the structure.
>
> https://www.dropbox.com/sh/y8wgl56qdw1ez9s/AADUtuIxeoIve4Q7K8uSyW7oa?dl=0
>
> Regards,
> Farideh
>
>
> On Wed, Dec 14, 2016 at 11:03 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> Do you have any fixed atoms in your system?
>>
>> Your system might have issues, e.g. Interlocked rings or similar. Check
>> the minimization trajectory in VMD.
>>
>> Were did you get the parameters for your polymer, are you sure they are
>> ok?
>>
>>
>>
>> If you want, sent your psf/pdb pair for us to check.
>>
>>
>>
>> Norman Geist
>>
>>
>>
>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *faride badalkhani
>> *Gesendet:* Mittwoch, 14. Dezember 2016 06:51
>> *An:* namd-l <namd-l_at_ks.uiuc.edu>
>> *Betreff:* namd-l: NVT and NPT simulationd
>>
>>
>>
>> Dear NAMD Users,
>>
>> My goal is to compare the microstructure of two different polymer using
>> MD simulations. For the first group of structures I had to perform a few
>> steps of NVT before NPT simulations (because they did not get equilibrate
>> well and this was your suggestion). But for the second group it is
>> completely different because there is no problem when I run NPT immediately
>> after minimization. But when I use the minimization+NVT+NPT I got low
>> global count error!
>>
>> I decreased the time step to 1 fs and reduced the number of processors
>> but nothing changed. Finally, I increased the box size. In this case the
>> NPT run is performed for about 6 ns and after that I get "Atom moving too
>> fast" error. I read the NAMD troubleshooting and check the mentioned atom
>> but there is nothing wrong with it.
>>
>> Now I want to know how can I overcome this error?
>>
>> IS there any necessity to reach equilibrium in the same way for both
>> groups?
>>
>> Regards,
>>
>> Farideh
>>
>
>

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