From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 17 2013 - 12:12:21 CDT
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
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) ?
2013/9/17 Aron Broom <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>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 :(
>> 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
>>> 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****
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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