Dear Amber,
I am performing multiple equilibration with random seed.
My question is it my command below right to perform the equlibration,
specifically, do I have to provide -c heat3.rst and -ref heat3.rst?
My thought is that because I use random seed, so there will be no -c and
-ref,
please correct me if I am wrong.
Here is the command I used:
pmedmd.cuda -O -i eq1.in -o eq1.out -p sol.prmtop -r eq1.rst -x eq1.nc -c
heat3.rst -ref heat3.rst &
The second question, I have three step equlibration under NPT ensemble with
different restraint of each equlibration. My intention is to perform
multiple MD simulation, and I think
I just use the random seed option for first equlibration, not in the second
and third ones.
Please correct me if my understanding is wrong.
My input file for first equilivration is:
Equilibration stage 1, 300K, 1 atm
&cntrl
imin=0,ntx=1,irest=0,
ntpr=100,ntwr=100,ntwx=100, ig=47309
nstlim=50000,dt=0.001,
ntt=3,gamma_ln=1,temp0=300,tempi=300,
ntb=2,ntp=1,pres0=1,taup=2,
cut=9,ntf=2,ntc=2,
ntr=1,restraintmask=':1-555.CA,C,N',restraint_wt=3,
/
Thank you.
Nadaafiva
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Received on Wed Jul 15 2020 - 21:00:03 PDT
