I don't see any gradual warming - your first run doesn't slowly heat,
and your final run starts with irest=0 so no velocities.
Bill
On 4/12/17 10:03 PM, Jorgen Simonsen wrote:
> Hi all,
>
> I am having an issue with the temperature after I have slowly heated up the
> system:
>
> 100ps MD with res on protein
>
> &cntrl
>
> imin = 0,
>
> irest = 0,
>
> ntx = 1,
>
> ntb = 1,
>
> cut = 10.0,
>
> ntr = 1,
>
> ntc = 2,
>
> ntf = 2,
>
> tempi = 0.0,
>
> temp0 = 300,
>
> ntt = 3,
>
> gamma_ln = 1.0,
>
> nstlim = 50000, dt = 0.002
>
> ntpr = 5000, ntwx = 5000, ntwr = 5000
>
> /
>
> Keep protein fixed with weak restraints
>
> 50.0
>
> RES 1 40
>
> END
>
> END
>
>
>
> I use the sander.MPI
>
>
> mpirun -np 16 ~/amber14/bin/sander.MPI -O -i md_disulfides.in -p
> solv.prmtop -c heat.rst -r md.rst
>
>
> with the following md input file:
>
>
> 10ps MD
>
> &cntrl
>
> imin = 0, irest = 0, ntx = 1, iwrap=1,
>
> ntb = 2, pres0 = 1.0, ntp = 1,
>
> taup = 2.0,ig=-1,
>
> cut = 10.0, ntr = 0,
>
> ntc = 2, ntf = 2,
>
> tempi = 300, temp0 = 300,
>
> ntt = 3, gamma_ln = 1.0,
>
> nstlim = 10000000, dt = 0.002,
>
> ntpr = 5000, ntwx = 5000, ntwr = 5000
>
> /
>
> I do want to start from random seeds to get indenpendent runs so I set the
> ig=-1 but still I would expect to be close to the equilibrated system.
>
> but from the first round I get the following error/ warning
>
>
> NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 440.42 PRESS =
> -621.5
>
> Etot = -19730.8465 EKtot = 8077.7368 EPtot =
> -27808.5832
>
> BOND = 105.8078 ANGLE = 205.4744 DIHED =
> 473.4839
>
> 1-4 NB = 130.7175 1-4 EEL = 2395.4889 VDWAALS =
> 3606.5258
>
> EELEC = -34726.0816 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> EKCMT = 2504.5210 VIRIAL = 4159.2641 VOLUME =
> 123313.0860
>
> Density =
> 0.7475
>
> Ewald error estimate: 0.6640E-04
>
> ------------------------------------------------------------------------------
>
>
> ***** Processor 0
>
> ***** System must be very inhomogeneous.
>
> ***** Readjusting recip sizes.
>
> In this slab, Atoms found: 1415 Allocated: 1412
>
>
> any help appreciated - thanks!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 12 2017 - 22:30:04 PDT
