Dear All,
I am trying to set a constant pH run. I simply followed Amber 14 manual to
create input files. Here are the steps I followed;
1-changed GLU, ASP and HIS to GL4, AS4 and HIP, respectively.
2-created prmtop and inpcrd files
3-run cpinutil.py -igb 2 -resname AS4 GL4 HIP -p prmtop -op new.prmtop >
cpin
4- run the simulation;
pmemd.cuda -O -i 01_min.in -o 01_min.out -p final.prmtop -c
1HXW-full.inpcrd -r 01_Min.rst -inf 01_Min.mdinfo
pmemd.cuda -O -i md-langevin.mdin -p final.prmtop -c 01_Min.rst -cpin cpin
Here are the input files for minimization and equilibration
Minimize
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=50000,
ncyc=25000,
ntpr=1000,
ntwx=0,
cut=10.0,
/
npt md simulation with langevin thermostat and monte carlo barostat
&cntrl
ioutfm = 1, ! binary trajectory
ntwprt = 3162, ! write protein and ion atoms only
ntpr = 100000, ! energy every 100ps
ntwr = 100000, ! restart every 100 ps
ntwx = 100, ! trajectory every 0.1 ps
dt = 0.001, nstlim = 100000000, ! 100 ns total simulation
ntt = 3, temp0 = 310, tempi = 310, gamma_ln = 2, ig=-1, ! thermostat
ntp = 1, barostat = 2, ! barostat
cut = 10.0, ! cutoff
icnstph=2,ntcnstph=100,ntrelax=200,solvph=4.5,saltcon=0.1,ntc=2,ntf=2 !
constant pH
/
Here, the problem is that nvidia-smi command returns GPU Volatile uitl=0%,
so I ugess the GPU's are not used. So far I have never faced with this
problem and all my other simulations (without constant pH option) are
running smoothly. As far as I know pmemd.cuda supports constant pH
simulations, but I am confused. Is there anything that I am missing?
All the best,
Batuhan
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Received on Mon Nov 10 2014 - 12:30:02 PST
