From: amin_at_imtech.res.in
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.
Regards.
Amin.
# To run this script type: namd2 <filename>
# modified
# Based on the NAMD-VMD online tutorial
#
# Set reusable variables
set structure pep_lys_met_ions
# input files
amber on
ambercoor $structure.inpcrd
parmfile $structure.prmtop
#restart
bincoordinates prod1/restart.coor
binvelocities prod1/restart.coor
extendedSystem prod1/restart.xsc
firsttimestep 7135000
#for amber
exclude scaled1-4
rigidbonds all
readexclusions yes
1-4scaling 0.833333333333
scnb 2.0
zeromomentum on
ljcorrection on
watermodel tip4
#output files
outputname prod2/heat_out
binaryoutput on
restartname prod2/restart
restartfreq 1000 # generation of restart files every
# 1000 x timestep fs
binaryrestart yes
dcdFile prod2/prod2.dcd
dcdFreq 1000 # writting dcd every 200 x timesteps fs
outputEnergies 1000
outputTiming 1000
xstFreq 1000
#time and multiple-timesteps parameters
#numsteps 1.0
timestep 2.0 #femto-seconds (fs)
stepsPerCycle 10
nonBondedFreq 1
fullElectFrequency 1
#simulation space partitioning
switching off
switchDist 10
cutoff 12
pairlistdist 13.5
COMmotion no
dielectric 1.0
useSettle on
# Particle Mesh Ewald parameters:
# a full electrostatics method for use with
# periodic boundary conditions
Pme on
PMEGridSpacing 1.0
wrapAll on
langevin on
langevinDamping 10
langevinTemp 300
langevinHydrogen off
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 300
useGroupPressure yes
useFlexibleCell no
useConstantArea no
run 4000000
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
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
> ERROR
>
> There are hundreds of such lines. After these lines the simulation runs and I can't see anything obviously wrong with the results.
>
> Regards.
>
> Amin.
>
> 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.
>
> Amin.
>
> 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?
>
> Regards.
>
> Amin.
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