From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 05 2015 - 08:56:36 CST
I can’t tell if these ERROR lines point out a real problem. It seems that one of the file reading plugins output this error on some lines it doesn’t like without further information, maybe blank lines in the prmtop or pdb or some encoding issues. You should carefully check the results and check for future jobs under which circumstances this issue arises.
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: Montag, 5. Januar 2015 14:35
An: Norman Geist
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: AW: AW: AW: namd-l: warnings while using amber files
I am very sorry I pasted an old config file which had .coor file as velocities. I noticed this mistake after a few runs and corrected it. I still get the same error lines.
My restart frequency is so low because the cluster I work on has very little disk space. Generally only 2-3 gb is free. So my simulations very frequently end prematurely due to insufficient disk space to write output files.
Thanks a lot for pointing out the problems in cutoff. I will make these changes in my config file.
If the config file looks fine to you (except the .coor as velocities issue, which I have corrected without any effect on the error lines), would it be safe to assume that these lines having ERROR written are innocuous.
Thanks for the help.
Amin.
On 2015-01-05 18:05, Norman Geist wrote:
Hey,
seems you use a *.coor as velocities, maybe that’s the problem. (see <-- below)
Btw. your restartfreq is way too low, you should raise it to 100000 or more as writing restart files is expensive and currently you write one every few seconds. Also your cutoff is unnecessarily high. Usually one uses cutoff=10, switchdist=9, parilistdist=14.
Mit freundlichen Grüßen
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: Montag, 5. Januar 2015 11:40
An: Norman Geist
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: AW: AW: namd-l: warnings while using amber files
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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