Hi Elvis,
Are you sure you are running AMBER 16 and not inadvertently an earlier version that doesn't support the barostat keyword?
Can you post your mdin and mdout files please.
All the best
Ross
> On Apr 27, 2017, at 2:53 AM, Elvis Martis <elvis.martis.bcp.edu.in> 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 _______________________________________________
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Received on Thu Apr 27 2017 - 05:00:03 PDT
