[AMBER] Constant pH MD with CUDA not working

From: BATUHAN KAV <bkav13.ku.edu.tr>
Date: Mon, 10 Nov 2014 22:05:55 +0200

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 >
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


npt md simulation with langevin thermostat and monte carlo barostat
  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,
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Received on Mon Nov 10 2014 - 12:30:02 PST
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