From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Dec 15 2016 - 02:20:28 CST
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 <mailto: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 <mailto: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> [mailto: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 <mailto: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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