[AMBER] Questions on random seed

From: Nada Afiva <nadaafiva.gmail.com>
Date: Thu, 16 Jul 2020 10:35:37 +0700

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
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
 ntpr=100,ntwr=100,ntwx=100, ig=47309

Thank you.
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Received on Wed Jul 15 2020 - 21:00:03 PDT
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