Re: charm-gui membrane builder

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Sep 17 2013 - 14:26:09 CDT

- If you get errors during system preparation, you should stop and fix
them rather than just proceeding if nothing happened. A non-integer charge
is obviously not OK. Neither are protons floating around. Neither is
getting PME errors during minimization.
- If you ignore the above advice and get errors when starting (or running)
your simulation, it seems logical that the earlier errors during system
preparation are at fault, so then you have to go back and fix your system
preparation errors rather than dumping your simulation error message on
the mailinglist (without even mentioning the earlier errors!) and wasting
everyone's time trying to pry the cause of the problem out of you. Your
behavior is inconsiderate and impolite.

On 09/17/2013 01:12 PM, James Starlight wrote:
> 1) The possible source of error with non-integer charge could arise from
> protonation state set to some titrable residues (e.g I've chosen one asp
> and another glu to be protonated by means of psfgen script)
>
>
> but during visualization I've realized that two new added protons looks
> like separate atoms. Also during minimization of such system I've obtained
> some erros with PME so I suppose that such sustem have been prepared with
> errors initially)
>
> 2) Another problem with PSF file generated by psfgen. I've tried to load
> this psf with the membnrane.pdb (both files created by charm-gui) to vmd
> and obtained error
>
> psfgen) Created by CHARMM version 36 1
> psfgen) clearing structure, preserving topology and aliases
> psfgen) reading structure from psf file membrane.psf
> psfgen) Error processing bonds
>
> does it possible to make new PSF via psfgen for membrane.pdb (Assuming
> that my membrane consist of popc pope tip3p as well as ions) ?
>
> James
>
>
>
> 2013/9/17 Aron Broom <broomsday_at_gmail.com <mailto:broomsday_at_gmail.com>>
>
> if you have non-integer net charge for your system, that suggests
> there may be more important general problems with your system
> topology. In general, the forcefields tend to be setup in such a way
> as to give integer or very close to integer values.
>
> You may want to inspect all the partial charges and see that they both
> make sense, and that each individual molecule in your system has an
> integer charge (i.e. find the molecule that doesn't)
>
>
> On Tue, Sep 17, 2013 at 1:33 AM, James Starlight
> <jmsstarlight_at_gmail.com <mailto:jmsstarlight_at_gmail.com>> wrote:
>
> 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
> <mailto: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>
> [mailto: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 <mailto: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____
>
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>

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