On Fri, Oct 16, 2015 at 12:13 PM, Guqin Shi <shi.293.osu.edu> wrote:
> Hi all!
>
> recently I want to do multiple independent runs by assigning different
> velocities to each run.
>
> So I have three stages for each run, eq1 for heating up, eq2 for pressure
> relaxation, and then run at NPT conditions. The assignment of velocites is
> at eq1 stage and below is the input:
>
> *Heating up the system equilibration stage -- only water is mobile*
> * &cntrl*
> * nstlim=100000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000,
> ntwx=500,*
> * tempi =0.0, temp0=300.0, ntt=1, tautp=2.0, ig=-1,*
> * ntb=1, ntp=0,*
> * ntc=2, ntf=2,*
> * nrespa=1,*
> * ntr=1,*
> * iwrap=1,*
> */*
> *Keep protein and ligand fixed*
> *50.0*
> *RES 1 100*
> *END*
> *END*
>
>
> However, I noticed that each run are IDENTICAL in all .out, .crd, and .rst
> files. So I realize the ig flag didn't work at all. Maybe I didn't fully
> understand the sentence in manual "The MD starting velocity is dependent on
> the random number generator seed if NTX .lt. 3 .and. TEMPI .ne. 0.0." Can
> anybody help illustrate how to correctly use ig flag? It seems ig=-1
> doesn't work if I have ntt=1 and tempi=0.0...? So in my case, what's the
> best way to assign random velocities in each run? How about assigning a
> number to ig? Do I need to change it for each run? It should be a very
> simple one but I have no experience dealing with it before.. Thanks for
> your time!
>
​What Ross said was correct. The physical explanation is simple -- an
initial temperature of 0 can only be achieved when all velocities are
zero. There is no randomness in that.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 16 2015 - 10:00:04 PDT
