This was way back in the day, a student forgot to set ig (or forgot to change the ig value, can’t remember which) and ran a triplicate simulation. We noticed that something was odd as the hydrogen bond and RDF analyses data produced identical values. Turned out that when you opened the trajectory data files in vmd, they were an exact overlay of each other.
So at least back then (2010/2011, can’t remember which amber version we were using then) starting from the same PRMTOP and IMPCRD files using other no randomisation (ig) or with the same random number (ig) produced no variation in the calculated trajectories in three separate replicates. So I would guess that starting from a RST file with no randomisation would produce identical trajectories, although I have not tried this myself.
Best regards
// Gustaf
> On 22 Jan 2020, at 11:53, Abdullah Bin Faheem <Abdullahbinfaheem.hotmail.com> wrote:
>
> Dear AMBER users,
>
> Is it possible to get the same output trajectory file if I use the same topology and restart file?
> Meaning if I run two MD runs in parallel, can I get the same xyz (or atleast very close) coordinates being written in the output coordinate file if I use the same restart and topology file? This is the input file I used initially (I am currently using AMBER 12):
>
> NPT ensemble simulation of 512 Acetonitrile molecules
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntpr = 500, ntave = 1000,
> ntwr = 500, ntwe = 50, ntwx = 5000,
> ntf = 2, ntc = 2, ntb = 2, cut = 12.0, nsnb = 10,
> nstlim = 100000, dt = 0.001, tempi = 298.0, temp0 = 298.0,
> ntt = 3, tautp = 1.0, ntp = 1, pres0 = 1.0, taup = 1.0,
> ioutfm=1, gamma_ln=1,
> &end
>
> But I've also tried using an NVT ensemble (ntb = 1, ntp = 0, ntt = 3, gamma_ln = 1) and NVT ensemble with a weak Berenden thermostat (ntb = 1, ntp = 0, ntt = 1, tautp = 10), I also didn't use the the "ig=-1" option so both runs used the same seed value i.e. "ig=71277".
>
> Thank you in advance.
> Best Regards,
> Abdullah Bin Faheem
> _______________________________________________
> 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 Jan 22 2020 - 06:00:03 PST
