Dear Users:
I am running a standard simulation with amber. The first segment was run for 8 microseconds. After about 2 microseconds I observed the formation of a salt-bridge that remained stable until the end of the first 8 microsecond segment. Upon restarting, this salt bridge is stable for the first 1 nanosecond but breaks after 1.6 nanoseconds. I realize that this could just be a coincidence and that the trajectories are stochastic, but I wanted to check to see if anybody can take a look at my -i input file to see if I did something that could have jolted the system at the beginning of the restart (stable for 6 us and then breaking in less than 1/1000th of that time immediately after a restart).
### Here it the command that I used for the restart
mpirun -np 4 ${AMBERHOMEDGX}/bin/pmemd.cuda.MPI -i md_restart.in -o MD2.out -p this.prmtop -c PART1/MD1.rst -r MD2.rst -x MD2.mdcrd -inf MD2.info -l MD2.log
### Here it the .in file that I used for the restart
A NPT simulation for common production-level simulations -- params generally from Charmm-gui + some modifications by CN
&cntrl
imin=0, ! No minimization
irest=1, ! ires=1 for restart and irest=0 for new start
ntx=5, ! ntx=5 to use velocities from inpcrd and ntx=1 to not use them
ntb=2, ! constant pressure simulation
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
temp0=310.0, ! Target temperature
tempi=310.0, ! Initial temperature -- has no effect if ntx>3
! Potential energy control
cut=12.0, ! nonbonded cutoff, in Angstroms
fswitch=10.0, ! for charmm.... note charmm-gui suggested cut=0.8 and no use of fswitch
! MD settings
nstlim=2000000000, ! 2B steps, 8 us total
dt=0.004, ! 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=50000, ! Print energy frequency
ntwx=50000, ! Print coordinate frequency
ntwr=500000, ! Print restart file frequency
! 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=2, ! Berendsen... change to 2 for MC barostat
ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.01325, ! Target external pressure, in bar
taup=4, ! Berendsen coupling constant (ps)
comp=45, ! compressibility
! 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='SOL', ! Water residues are named TIP3
owtnm='OW', ! Water oxygens are named OH2
hwtnm1='HW1',
hwtnm2='HW2',
&end
&ewald
! nfft1 = 72, nfft2 = 72, nfft3 = 72, order = 6,
vdwmeth = 0,
&end
### The .in file for this restart is the same as the original .in file, with changes to do a restart
$ diff md.in md_restart.in
5,6c5,6
< irest=0, ! ires=1 for restart and irest=0 for new start
< ntx=1, ! ntx=5 to use velocities from inpcrd and ntx=1 to not use them
---
> irest=1, ! ires=1 for restart and irest=0 for new start
> ntx=5, ! ntx=5 to use velocities from inpcrd and ntx=1 to not use them
## Here I show that reported temperatures look continuous
$ grep TEMP PART1/MD1.out|tail
NSTEP =********* TIME(PS) = 7998599.821 TEMP(K) = 310.59 PRESS = 0.0
NSTEP =********* TIME(PS) = 7998799.821 TEMP(K) = 307.46 PRESS = 0.0
NSTEP =********* TIME(PS) = 7998999.821 TEMP(K) = 307.98 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999199.821 TEMP(K) = 309.81 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999399.821 TEMP(K) = 309.58 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999599.821 TEMP(K) = 310.97 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999799.821 TEMP(K) = 309.77 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999999.821 TEMP(K) = 310.10 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999999.821 TEMP(K) = 310.34 PRESS = 0.0
NSTEP =********* TIME(PS) = 7999999.821 TEMP(K) = 1.51 PRESS = 0.0
$ grep TEMP MD2.out|head
NSTEP = 50000 TIME(PS) = 8000199.821 TEMP(K) = 311.68 PRESS = 0.0
NSTEP = 100000 TIME(PS) = 8000399.821 TEMP(K) = 310.55 PRESS = 0.0
NSTEP = 150000 TIME(PS) = 8000599.821 TEMP(K) = 311.33 PRESS = 0.0
NSTEP = 200000 TIME(PS) = 8000799.821 TEMP(K) = 312.86 PRESS = 0.0
NSTEP = 250000 TIME(PS) = 8000999.821 TEMP(K) = 310.22 PRESS = 0.0
NSTEP = 300000 TIME(PS) = 8001199.821 TEMP(K) = 309.99 PRESS = 0.0
NSTEP = 350000 TIME(PS) = 8001399.821 TEMP(K) = 310.99 PRESS = 0.0
NSTEP = 400000 TIME(PS) = 8001599.821 TEMP(K) = 309.74 PRESS = 0.0
NSTEP = 450000 TIME(PS) = 8001799.821 TEMP(K) = 310.17 PRESS = 0.0
NSTEP = 500000 TIME(PS) = 8001999.821 TEMP(K) = 308.80 PRESS = 0.0
## And similarly for Etot:
$ grep Etot PART1/MD1.out|tail
Etot = -63093.8036 EKtot = 26000.9648 EPtot = -89094.7685
Etot = -63064.5890 EKtot = 25739.0430 EPtot = -88803.6320
Etot = -63168.4643 EKtot = 25782.2344 EPtot = -88950.6987
Etot = -62854.3741 EKtot = 25935.2207 EPtot = -88789.5948
Etot = -63053.0076 EKtot = 25916.0293 EPtot = -88969.0369
Etot = -62538.2596 EKtot = 26032.4922 EPtot = -88570.7518
Etot = -63057.3811 EKtot = 25932.4180 EPtot = -88989.7991
Etot = -62623.0444 EKtot = 25960.0859 EPtot = -88583.1303
Etot = -62752.7520 EKtot = 25979.6039 EPtot = -88732.3559
Etot = 218.8284 EKtot = 126.5421 EPtot = 178.4276
$ grep Etot MD2.out|tail
Etot = -63095.3276 EKtot = 25909.5820 EPtot = -89004.9097
Etot = -62271.7051 EKtot = 26122.3516 EPtot = -88394.0566
Etot = -62810.7159 EKtot = 25903.6602 EPtot = -88714.3761
Etot = -62478.0905 EKtot = 26064.9023 EPtot = -88542.9928
Etot = -63141.8379 EKtot = 25768.9941 EPtot = -88910.8321
Etot = -62729.8675 EKtot = 25990.6504 EPtot = -88720.5179
Etot = -62653.5125 EKtot = 26076.0547 EPtot = -88729.5672
Etot = -62502.7829 EKtot = 26009.7539 EPtot = -88512.5368
Etot = -62820.8625 EKtot = 26021.7812 EPtot = -88842.6437
Etot = -63146.8054 EKtot = 25852.2715 EPtot = -88999.0769
*** Note: the low values at the end of Part1 for temperature and energies are picking up a line that is showing RMS fluctuations, not values
Thank you very much for your help
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 16 2016 - 11:00:02 PST
