On Fri, Nov 13, 2015 at 3:03 PM, Himanshu Joshi <himanshuphy87.gmail.com>
wrote:
> Dear Ross,
> Thank you very much for the clarification.
> .
> Regarding the ntr=1 question, here is my input file followed by some lines
> from mdout file.
> I am running pmemd.cuda.MPI with recent updates on AMBER14. After the
> anomaly, I am
> trying some cpu runs also, I will update you soon with the proceedings.
>
> Lipid equilibration
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> ntc=2,
> ntf=2,
> tol=0.0000001,
> nstlim=1000000,
> ntt=3,
> gamma_ln=1.0,
> temp0=300.0,
> ntpr=5000,
> ntwr=5000,
> ntwx=10000,
> dt=0.002,
> ig=-1,
> ntb=2,
> ntp=2,
> cut=10.0,
> ioutfm=1,
> ntxo=2,
> ntr=1,
> /
> /
> &ewald
> skinnb=5, ! Increase skinnb to avoid skinnb errors
>
This will potentially hurt performance quite a bit. I would suggest
keeping the default. I know this may cause initial NpT simulations to
crash occasionally at the beginning, but these errors should stop after the
equilibration phase when the box stops shrinking so rapidly.
> /
> Hold complex fixed
> 10.0 ! Force constant (kcal/(mol Angstroms^2))
> RES 1 684
> END
> END
>
>
>
>
> NSTEP = 5000 TIME(PS) = 115.000 TEMP(K) = 300.59 PRESS =
> -19.2
> Etot = -1354836.4560 EKtot = 232224.1094 EPtot =
> -1587060.5653
> BOND = 11059.7680 ANGLE = 35413.1898 DIHED =
> 30219.4001
> 1-4 NB = 10644.2777 1-4 EEL = -39686.4662 VDWAALS =
> 138379.2243
> EELEC = -1777768.0290 EHBOND = 0.0000 RESTRAINT =
> 4678.0700
> EAMBER (non-restraint) = -1591738.6354
> EKCMT = 94470.4812 VIRIAL = 96232.2583 VOLUME =
> 4260611.2260
> Density =
> 0.9639
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 10000 TIME(PS) = 125.000 TEMP(K) = 301.34 PRESS =
> -6.9
> Etot = -1355582.3661 EKtot = 232804.5312 EPtot =
> -1588386.8973
> BOND = 11119.2994 ANGLE = 35156.3936 DIHED =
> 30306.2670
> 1-4 NB = 10634.9034 1-4 EEL = -39622.6550 VDWAALS =
> 137181.2647
> EELEC = -1777996.0569 EHBOND = 0.0000 RESTRAINT =
> 4833.6864
> EAMBER (non-restraint) = -1593220.5838
> EKCMT = 94996.1801 VIRIAL = 95628.3471 VOLUME =
> 4219058.6682
> Density =
> 0.9734
>
> ------------------------------------------------------------------------------
>
There's nothing here to suggest that the simulation is not stable with
restraints.
You will have to be more specific. When do the instabilities occur?
Randomly during the simulation? Immediately (or very quickly) after
restart?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 13 2015 - 13:30:04 PST
