Try deleting the comment part of the "barostat=1," line - perhaps the
"...." is confusing namelist.
Bill
On 4/26/17 11:53 PM, Elvis Martis wrote:
> Hi
> Sorry the previous mail had formatting errors. Have a look at this input file
> A NPT simulation for common production-level simulations >> comment of blank line
> &cntrl >> see this change
> imin=0, ! No minimization
> irest=1, ! This IS a restart of an old MD simulation
> ntx=5, ! So our inpcrd file has velocities
>
> ! Temperature control
> ntt=3, ! Langevin dynamics
> gamma_ln=1.0, ! Friction coefficient (ps^-1)
> temp0=303.15, ! Target temperature
>
> ! Potential energy control
> cut=8.0, ! nonbonded cutoff, in Angstroms
>
> ! MD settings
> nstlim=500000, ! 500K steps, 1 ns total
> dt=0.002, ! time step (ps)
>
> ! SHAKE
> ntc=2, ! Constrain bonds containing hydrogen
> ntf=2, ! Do not calculate forces of bonds containing hydrogen
>
> ! Control how often information is printed
> ntpr=1000, ! Print energies every 1000 steps
> ntwx=1000, ! Print coordinates every 1000 steps to the trajectory
> ntwr=10000, ! Print a restart file every 10K steps (can be less
> frequent)
> ! ntwv=-1, ! Uncomment to also print velocities to trajectory
> ! ntwf=-1, ! Uncomment to also print forces to trajectory
> ntxo=2, ! Write NetCDF format
> ioutfm=1, ! Write NetCDF format (always do this!)
>
> ! Wrap coordinates when printing them to the same unit cell
> iwrap=1,
>
> ! Constant pressure control. Note that ntp=3 requires barostat=1
> barostat=1, ! Berendsen... change to 2 for MC barostat
> ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
> pres0=1.0, ! Target external pressure, in bar
> taup=0.5, ! Berendsen coupling constant (ps)
>
> ! Constant surface tension (needed for semi-isotropic scaling).
> Uncomment
> ! for this feature. csurften must be nonzero if ntp=3 above
> csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
> gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
> ninterface=2, ! Number of interfaces (2 for bilayer)
>
> ! Set water atom/residue names for SETTLE recognition
> watnam='WAT', ! Water residues are named WAT
> owtnm='O', ! Water oxygens are named O
> /
> >> added blank line at the end of input file
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Elvis Martis
> Sent: Thursday, April 27, 2017 12:22 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: RE: [AMBER] barostat=1 error at Stampede
>
>
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Tarsis [mailto:tarsis.ferreira.gmail.com]
> Sent: Thursday, April 27, 2017 1:40 AM
> To: amber.ambermd.org
> Subject: [AMBER] barostat=1 error at Stampede
>
> Hi, when I try to run an MD at stampede using barostat=1 I get the error
> bellow. If I comment the line out it runs fine. Anyone knows how to fix this? The input script follows the error message. thanks in advance.
>
> forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 5, file /work/step7_production.mdin, line 36, position 12
>
> Image PC Routine Line Source
>
>
> libintlc.so.5 00002AB13814DA1E Unknown Unknown Unknown
>
> libintlc.so.5 00002AB13814C4B6 Unknown Unknown Unknown
>
> libifcore.so.5 00002AB13704F01E Unknown Unknown Unknown
>
> libifcore.so.5 00002AB136FBEB1E Unknown Unknown Unknown
>
> libifcore.so.5 00002AB136FBE01D Unknown Unknown Unknown
>
> libifcore.so.5 00002AB137000BDB Unknown Unknown Unknown
>
> pmemd 0000000000632D4F Unknown Unknown Unknown
>
> pmemd 000000000055EE14 Unknown Unknown Unknown
>
> pmemd 000000000055ADFC Unknown Unknown Unknown
>
> pmemd 0000000000402E6C Unknown Unknown Unknown
>
> libc.so.6 000000300041ED1D Unknown Unknown Unknown
>
> pmemd 0000000000402D69 Unknown Unknown Unknown
>
> #################
> Input
>
> A NPT simulation for common production-level simulations >> comment of blank line &cntrl >> see this change
> imin=0, ! No minimization
> irest=1, ! This IS a restart of an old MD simulation
> ntx=5, ! So our inpcrd file has velocities
>
> ! Temperature control
> ntt=3, ! Langevin dynamics
> gamma_ln=1.0, ! Friction coefficient (ps^-1)
> temp0=303.15, ! Target temperature
>
> ! Potential energy control
> cut=8.0, ! nonbonded cutoff, in Angstroms
>
> ! MD settings
> nstlim=500000, ! 500K steps, 1 ns total
> dt=0.002, ! time step (ps)
>
> ! SHAKE
> ntc=2, ! Constrain bonds containing hydrogen
> ntf=2, ! Do not calculate forces of bonds containing hydrogen
>
> ! Control how often information is printed
> ntpr=1000, ! Print energies every 1000 steps
> ntwx=1000, ! Print coordinates every 1000 steps to the trajectory
> ntwr=10000, ! Print a restart file every 10K steps (can be less
> frequent)
> ! ntwv=-1, ! Uncomment to also print velocities to trajectory
> ! ntwf=-1, ! Uncomment to also print forces to trajectory
> ntxo=2, ! Write NetCDF format
> ioutfm=1, ! Write NetCDF format (always do this!)
>
> ! Wrap coordinates when printing them to the same unit cell
> iwrap=1,
>
> ! Constant pressure control. Note that ntp=3 requires barostat=1
> barostat=1, ! Berendsen... change to 2 for MC barostat
> ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
> pres0=1.0, ! Target external pressure, in bar
> taup=0.5, ! Berendsen coupling constant (ps)
>
> ! Constant surface tension (needed for semi-isotropic scaling).
> Uncomment
> ! for this feature. csurften must be nonzero if ntp=3 above
> csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
> gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
> ninterface=2, ! Number of interfaces (2 for bilayer)
>
> ! Set water atom/residue names for SETTLE recognition
> watnam='WAT', ! Water residues are named WAT
> owtnm='O', ! Water oxygens are named O
> /
> >> added blank line at the end of input file _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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>
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Received on Thu Apr 27 2017 - 00:30:02 PDT
