AW: Atoms moving too fast with NAMD/Amber

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jul 27 2012 - 03:39:33 CDT

Which one ^^

Norman Geist.

> -----Urspr√ľngliche Nachricht-----
> Von: Francesco Pietra [mailto:chiendarret_at_gmail.com]
> Gesendet: Freitag, 27. Juli 2012 09:13
> An: Norman Geist
> Betreff: Re: namd-l: Atoms moving too fast with NAMD/Amber
>
> Yes, it was just the case that you prospected. Thanks
> francesco
>
> On Thu, Jul 26, 2012 at 8:42 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
> > Hi,
> >
> > I also use the amber ff and the atoms moving too fast error is most
> of cases due to an error of the box or simulation setup, not the ff
> itself. I think the most likely case is that you have overlapping or
> too close atoms. You should check the VDW energy in the minimization if
> there are 999999 energies. Also, check the settings of the constraints
> if you use some. I also had this error one time when I had a broken
> GPU, so if this is a GPU run, try another GPU to figure out.
> >
> > In general this error must come with high forces, so the first is to
> check the energies if their height fits to the systems size.
> >
> > Norman Geist.
> >
> >> -----Urspr√ľngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Francesco Pietra
> >> Gesendet: Donnerstag, 26. Juli 2012 07:49
> >> An: NAMD
> >> Betreff: namd-l: Atoms moving too fast with NAMD/Amber
> >>
> >> In connection with the suggestions below, is any general protocol to
> >> follow when atoms move too fast with NAMD-CUDA when using Amber
> parm7
> >> ff (prmtop/inpcrd)? It is implied that I am facing this problem
> after
> >> succesful minimization and extreme care in settings for heating.
> >>
> >> thanks
> >> francesco pietra
> >>
> >> On Thursday 06 May 2010 12:32:13 ipsita basu wrote:
> >> > Thanks a lot for your reply. I tried timestep 1 before your reply
> and
> >> > the job was running fine without giving any error. But the
> structure
> >> > become distorted, it squeezes along z axis. Now according to your
> >> > reply I am fix the langevin temp to zero and heating the system
> >> > gradually by loop. This part is given below:
> >> > # gradual temp increase
> >> > run 1000
> >> > for { set TEMP 0 } { $TEMP <= 290 } {incr TEMP 1 } {
> >> > langevinTemp $TEMP
> >> > run 1000
> >> > I hope this will not disturb the structure.
> >> > Any suggestion from your end would be appreciated.
> >> >
> >>
> >> Mmmmh, you probably should double check your structure.
> >> I never ran into problems setting temperature, langevinTemp and
> >> LangevinPistonTemp to 303 Kelvin from start.
> >>
> >> Make sure to minimize your structure long enough.
> >> At one point it could be necessary to tune the minimization
> parameters
> >> (in
> >> case of bad contacts which are not removed during a normal
> >> minimization).
> >> Once I was forced to use CHARMM with the SD minimizer to get my
> >> structure
> >> minimized correctly (after this I could run the simulation in NAMD).
> >>
> >> To preserve the structure of you protein you should apply
> constraints
> >> to the
> >> protein backbone (C-Alphas, ~10 kcal/(mol*Angs^2)) and reduce them
> step
> >> by
> >> step. Something like this:
> >>
> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >> constraints on
> >> consref cons.pdb
> >> conskfile cons.pdb
> >> conskcol B
> >> constraintScaling 1.0
> >>
> >> # Minimization
> >> minimize 2000
> >> reinitvels $temp
> >>
> >> run 20000
> >> constraintScaling 0.5
> >
> >

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