Re: [AMBER] barostat=1 error at Stampede

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Thu, 27 Apr 2017 06:51:56 +0000

    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
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