From: amin_at_imtech.res.in
Date: Mon Jan 05 2015 - 07:34:30 CST
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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