Date: Mon Jan 05 2015 - 04:39:58 CST
Thanks for the reply. I get the same kind of error if I start a new run
or restart from a restart file. Initially I had restrained my protein
but now I don't have any restraints. But the error has remained
consistent with or without the restraints. Can this error be because of
some kind of communication issue between the nodes? I have pasted my
config file below.
# To run this script type: namd2 <filename>
# Based on the NAMD-VMD online tutorial
# Set reusable variables
set structure pep_lys_met_ions
# input files
restartfreq 1000 # generation of restart files every
# 1000 x timestep fs
dcdFreq 1000 # writting dcd every 200 x timesteps fs
#time and multiple-timesteps parameters
timestep 2.0 #femto-seconds (fs)
#simulation space partitioning
# Particle Mesh Ewald parameters:
# a full electrostatics method for use with
# periodic boundary conditions
On 2015-01-05 14:49, Norman Geist wrote:
> That's weird, I think one of your input files is corrupted or of wrong format. Maybe an additional pdb for constraints or fixed atom etc or a restart file?
> Norman Geist.
> VON: amin_at_imtech.res.in [mailto:amin_at_imtech.res.in]
> GESENDET: Montag, 5. Januar 2015 09:51
> AN: Norman Geist
> CC: namd-l_at_ks.uiuc.edu
> BETREFF: Re: AW: namd-l: warnings while using amber files
> Thanks. It's a relief that these warnings are harmless. The lines containing error have just "ERROR" written, nothing else e.g.
> Info: LONG-RANGE LJ: APPLYING ANALYTICAL CORRECTIONS TO ENERGY AND PRESSURE
> Info: LONG-RANGE LJ: AVERAGE A AND B COEFFICIENTS -1.42444e+06 AND -1325.18
> There are hundreds of such lines. After these lines the simulation runs and I can't see anything obviously wrong with the results.
> On 2015-01-05 12:12, Norman Geist wrote:
> I think we should see the ERROR lines, too, as the lines you have posted are not an error. NAMD just tells that it skipped unused sections of the parmtop.
> Norman Geist.
> VON: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] IM AUFTRAG VON amin_at_imtech.res.in
> GESENDET: Freitag, 26. Dezember 2014 04:55
> AN: Namd l
> BETREFF: Re: namd-l: warnings while using amber files
> I think I should add that I am using NAMD-2.9 x64 (ibverbs) and ambertools 14.
> On 2014-12-25 16:44, amin_at_imtech.res.in wrote:
> Dear all,
> I am trying to run a simulation with amber prmtop and inpcrd files made using tleap. I have used amber ff14sb force field. In the log file I get the following warnings:
> PARM file in AMBER 7 format
> Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS.
> Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
> Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY.
> Warning: Encounter 10-12 H-bond term
> Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED
> Warning: Found 32738 H-H bonds.
> Then I get many lines where only "ERROR" is written.
> Can someone please help me with this?
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:46 CST