From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 17 2013 - 00:33:30 CDT
Hi Norman!
I've already tried to increased
langevinPistonPeriod 200.
langevinPistonDecay 50.
up to
langevinPistonPeriod 400.
langevinPistonDecay 100.
but simulation have been crushed in any case
by the way the possible source of error could be due to non integer charge
that my system has.
Initialy I had protein with ligand with total charge +3 and neitralized
membrane produced by charm-gui (non charged lipids). After insertion of my
protein into membrane and re-ionization I have obtained total charge 0.45.
I have no idea how I could fix it yet :(
James
2013/9/16 Norman Geist <norman.geist_at_uni-greifswald.de>
> Hi James,****
>
> ** **
>
> if you’re using a barostat, consider increasing the relax/decay times, as
> fixed atoms lead to high forces due the coordinate rescaling which moves
> the non-fixed into the fixed atoms. Otherwise check your minimization log
> file for messages like “Moving xxx Atoms with bad contacts downhill” or
> even worse “Giving up on xxx Atoms with bad contacts”. If so, you might
> have some superimposed atoms in your structure. Also check if your
> minimization was run for long enough by plotting the TOTAL energy and see
> if it converged.****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *James Starlight
> *Gesendet:* Montag, 16. September 2013 14:08
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* Fwd: namd-l: charm-gui membrane builder****
>
> ** **
>
> Recently I've forced with new problem during simulation of the membrane
> protein.****
>
> Following Namd's tutorial I've built my system consisted of receptor
> embedded in the popc bilayer surrounded water and ions.
>
> After minimization I've launch first stage of equilibration (fixed all
> atoms excepts of the lipid tales)****
>
> this simulation have been crashed immediately with rattle errors.****
>
> than I've decreased timestep down to 0.3 and increased cutoffs up to 25
> (because namd told me than I should do it). Within this setup I can run my
> simulation but on each step I obtain
>
> ERROR: Margin is too small for 2 atoms during timestep 5001.
> ERROR: Incorrect nonbonded forces and energies may be calculated!****
>
> I have no any margin in my conf file so I have no idea how I can fix it
> and what possible source of errors.****
>
> Thanks for help****
>
> James****
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:44 CST