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 - 00:00:03 PDT
