Dear AMBER experts,
I have on my linux server AMBER16.
During MD production simulations the protein
has been drifting to the border of the periodic cell
with a tendency of going out of it.
I need your advice what a key parameter should I add
to the MD simulating script in order to prevent
the protein drifting out of the periodic cell?
See MD simulation details below.
Thank you,
Michael
The protein was solvated in octahedral
periodic cell applying TLEP procedure:
solvateoct mc TIP3PBOX 15
I used the following command lines to run production MD simulations:
setenv CUDA_VISIBLE_DEVICES '2,3'
nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i md_prod1.in -o md_prod6.out -p ../*.prmtop -c md_prod5.rst -x md_prod6.mdcrd -r md_prod6.rst -ref md_prod5.rst &
The production MD simulation script, md_run.in, is:
mc: 100 ns production phase MD
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 1.0,
cut = 10.0, iwrap = 1,
ntc = 2, ntf = 2,
tempi = 310.0, temp0 = 310.0,
ntt = 3, gamma_ln = 0.5,
nstlim = 50000000, dt = 0.002, barostat=2,
ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
/
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Received on Wed Sep 20 2017 - 02:30:01 PDT
