Good Evening,
I am attempting to run a simulation on a system of 400 residues, at pHs: 4,
5, 6, 7, 8, 9, 10, 11. There are 51 protonatable residues. I selected the
10 nearest the active site that I'm most concerned with. I used the H++
server, and generated models at each pH. This was done to try to correct
the more distant histidine protonation states. At low pH I would rather see
all the histidines protonated, versus at high pH. All eight systems ran at
relatively the same speed for the heating and equilibration phases.
Though something odd is happening. When I run the simulation at pH 4, I am
getting speeds of: 108 ns/day. At all other pHs (5 thru 11), I am getting
ranges from 10 ns/day to 45 ns/day. I thought it might be a hardware issue,
so I ran the pH 4 on a different card, and still got normal speeds. I ran
pH4 using a set ig value on two different nodes, and they ran at equal
speeds. I ran a few fo the other pHs on different cards (1080, 780,
Quadros..), and ran two copies with same igs. All of my input files are
identical (except for solvph parameter):
Explicit solvent constant pH MD
&cntrl
imin=0, irest=1, ntx=5, ntxo=2,
ntpr=20000, ntwx=20000,
nstlim=50000000, dt=0.002,
ntt=3, tempi=300,
temp0=300, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=8, iwrap=1,
ioutfm=1, icnstph=2, ntcnstph=100,
solvph=4.0, ntrelax=1000, saltcon=0.1,
/
I couldn't find anyone else on the listserv with a similar issue so figured
I'd post it. It appears as though in these other simulations there is a
pause when I do a "tail -f" on the output during the 2nd section. It hangs
here:
Ewald parameters:
I'm not sure if thats significant. the Ewald parameters are very similar
for all pH values...
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 64.697 Box Y = 81.032 Box Z = 83.653
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 64 NFFT2 = 84 NFFT3 = 84
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords =200400.000 ps
Number of triangulated 3-point waters found: 12712
Sum of charges from parm topology file = -0.00000016
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 1565040
| Integers 1861661
| Nonbonded Pairs Initial Allocation: 7358787
| GPU memory information (estimate):
| KB of GPU memory in use: 235748
| KB of CPU memory in use: 49631
If anyone else has any suggestions, I would appreciate it. I wish it were
possible to see or probe what exactly is causing pmemd to get choked up.
monitor a loop, etc.
Best Regards,
Andrew
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Received on Sun Sep 24 2017 - 00:00:02 PDT
