Dear Dr. David
Thanks again for your reply. I am simulating a protein monomer of 515
residues with a ligand and two cofactors. I want to run
multiple simulations to confirm the results I am getting from the
simulation. For that, I did serial minimization on cpu. After getting
minimized structure I did equilibrations (both nvt and npt) with restraints
on heavy atoms and finally with no restraints. For the production run,
I did simulation in 5 parts to get a 100ns simulation. For all of these
simulations, I did the first step of heating at ig=-1 then used rst file of
previous steps in proceeding simulations as mentioned in commands below:-
First step of minimization:-
Input:-
Min-01 minimize initial structure
&cntrl
imin=1, maxcyc=100000,
ntb = 1,
ntr = 1,
ntpr = 100,
ntwr = 100,
cut= 12.0,
restraint_wt=25.0,
restraintmask=':1-502',
/
mpirun pmemd.MPI -O -i min1.in -o min1.out -p complex_wild.prmtop -c
complex_wild.inpcrd -r min1.rst -ref complex_wild.inpcrd
Last step of minimization:-
MIN-06
&cntrl
imin=1, maxcyc=100000,
ntmin=1, ncyc=10000
ntb = 1,
ntpr = 100,
ntwr = 100,
cut= 12.0,
/
mpirun pmemd.MPI -O -i min7.in -o min7.out -p complex_wild.prmtop -c
min6.rst -r min7.rst -ref min6.rst
First step of heating :-
Heating up the system equilibration stage 1 50ps
&cntrl
imin=0, nstlim=100000, dt=0.0005, ntx=1, irest=0, ntpr=5000, ntwr=5000,
ntwx=5000,
tempi =0.0, temp0=50.0, ntt=3, tautp=2.0, ig=2 gamma_ln=1,iwrap = 1,
ntb=1, ntp=0, ntr=1,
ntc=2, ntf=2,
nrespa=2,
restraint_wt=25.0,
restraintmask=':1-502'
pmemd.cuda -O -i Heat_eq_v1.in -p complex_wild.prmtop -c min7.rst -r
Heat_eq_v1.rst -o Heat_eq_v1.out -x Heat_eq_v1.nc -ref min7.rst
First step of Pressure equilibration:-
Constant pressure constant temperature equilibration stage 1
&cntrl
imin=0, nstlim=100000, dt=0.0005, ntx=5, irest=1, ntpr=5000, ntwr=5000,
ntwx=
temp0=300.0, ntt=3, taup=2.0, gamma_ln=5,
ntb=2, ntp=1, pres0 = 1.0,
ntc=2, ntf=2,ntr=1,
nrespa=1,
&end
Group input for restrained atoms
25.0
RES 1 502
END
END
pmemd.cuda -O -i Pressure_eq_p1.in -p complex_wild.prmtop -c Heat_eq_v7.rst
-r Pressure_eq_p1.rst -x Pressure_eq_p1.nc -o Pressure_eq_p1.out -ref
Heat_eq_v7.rst
Production run 1:-
Constant pressure constant temperature production run
&cntrl
nstlim= 10000000, imin=0, dt=0.002, ntx=5, irest=1, ntpr=5000, ntwr=5000,
ntwx=5000
temp0=300.0, ntt=3, tautp=2.0, gamma_ln=5.0,
ntb=2, ntp=1,
ntc=2, ntf=2,
&end
pmemd.cuda -O -i Prod_20.in -p complex_wild.prmtop -c Pressure_eq_p6.rst -r
Prod_20.rst -x Prod_20.nc -o Prod_20.out
Please correct me further if I am wrong in the above-mentioned process.
Thanks in avdance.
Regards
Sadaf
On Thu, 25 Nov 2021 at 01:34, David A Case <david.case.rutgers.edu> wrote:
> On Thu, Nov 25, 2021, Sadaf Rani wrote:
>
> >I am running these simulations on
> >GPU. I am using the same combination as you mentioned .e.g. ntt=3 and
> >ig=-1. Does it mean that although the simulation has varying results the
> >convergence should be similar? Could you please give your comments on
> >it how should I proceed with the duplicate run of simulation? Either I
> need
> >to give the same seed number?
>
> If you want to check that two simulations give identical results, then,
> yes,
> you need explicitly set a seed (via ig) and keep it the same for the
> multiple runs. In fact, this is what we do in "stress tests" of GPU
> hardware, to make sure that the expected identical results are indeed
> found.
>
> To run replicated simulations to test convergence, stick with the default
> ig
> value of -1. Then the differences between (among) multiple runs is one
> measure of reproducibility, akin to re-running an experiment to look for
> noise in the outputs.
>
> I don't know anything about your system, but 20 ns of production is fairly
> short by modern standards. You should think about switching to barostat=2,
> which will be both faster and more in accord with a true canonical
> ensemble.
>
> ....dac
>
>
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Received on Wed Nov 24 2021 - 22:30:03 PST
