VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Mar 25 2018 - 20:44:48 CDT
- Next message: Denish Poudyal: "NAMD simulation"
- Previous message: The Cromicus Productions: "Re: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin"
- In reply to: Denish Poudyal: "i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster???"
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1) Writing a message in the subject line is just weird.
2) This is the VMD mailing list. You should post your question in the NAMD
mailing list. Hopefully with the content in the body and not subject line.
3) It is not recommended to run simulations on your laptop.
4) *The information you have provided is incomplete. Are you using a 2 fs
time step? How many cores are you using to run this simulation?*
5) Normal laptop computers are not designed for this type of work. It is
recommended that you switch to a desktop machine or preferably a cluster.
On Mon, Mar 26, 2018 at 2:22 PM, Denish Poudyal <qrystal45_at_gmail.com> wrote:
>
>
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> *Denish PoudyalCDPTU, Nepal*
>
-- Best, /A
- Next message: Denish Poudyal: "NAMD simulation"
- Previous message: The Cromicus Productions: "Re: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin"
- In reply to: Denish Poudyal: "i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster???"
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