Re: NVT and NPT simulationd

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Dec 15 2016 - 14:38:24 CST

Hi,

Kindly find the minimized structure in the following link:

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

Regards,
Farideh

On Thu, Dec 15, 2016 at 11:50 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> You have several overlong bonds in your structure, two of them cross each
> other, this might be unresolvable for the minimizer. Can you also supply
> the final structure after minimization?
>
>
>
> Norman Geist
>
>
>
> *Von:* faride badalkhani [mailto:farideh.khamseh_at_gmail.com]
> *Gesendet:* Mittwoch, 14. Dezember 2016 19:14
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Cc:* namd-l <namd-l_at_ks.uiuc.edu>
> *Betreff:* Re: namd-l: NVT and NPT simulationd
>
>
>
> 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
>
> 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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