Hi,
I am observing sampling issues with pmemd.cuda of Amber12 for a monomer
system. Currently, I am using ff9SB forcefield and an explicit solvent
model where the masses of solvent and side chains are rescaled by a factor
of 0.5. I have tested the performance of pmemd.MPI and pmemd.cuda. The
system is stable with pmemd.MPI version. The monomer was minimized and
sampled under NVT conditions for 50 ns using the following input files:
Minimization step1:
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
ntr = 1,
cut = 12.0,
/
Hold the protein weakly
10.0
RES 1 107
END
END
Minimization Step2
1REI: initial minimization of the system
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 1,
ntr = 0,
cut = 12.0
/
Generating initial velocities under NVT conditions:
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 12.0,
ntr = 1,
ntc = 2,
ntf = 2,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000,
tempi = 298.15,
temp0 = 298.15,
dt = 0.002,
ntpr = 1000,
ntwx = 1000,
ntwr = 1000,
/
keep the protein fixed with weak restraints
10.0
RES 1 107
END
END
Sampling process:
&cntrl
imin=0,
ntx=5,
irest=1,
ntc=2,
ntf=2,
nstlim=5000000,
ntt=3,
gamma_ln=1.0,
temp0=298.15,
ntpr=5000,
ntwr=5000,
ntwx=5000,
dt=0.002,
ig=-1,
ntb=1,
cut=12.0,
ioutfm=1,
/
The average RMSd over 50ns was 1.07 +/- 0.01 for the monomer when pmemd.MPI
was used. The structures at various intervals were visualized using VMD.
The 3D structure of the monomer was retained throughout the simulation.
Then, I have used pmemd.cuda in order to run the system for a longer
simulation time. The generation of initial velocities and sampling were
done using a similar input file that was used for pmemd.MPI. However, the
RMSd of the monomer just after 10 ps of the simulation was about 7.0
angstrom and keeps increasing all the way to 36.0 angstroms after 10 ns of
simulation. The tertiary structure of the monomer was lost and the protein
has denatured. So, I have tested the behavior of the system using 1 fs
time step. The system was stable until 10 ns of the simulation (RMSd 1.5
+/- 0.3). But the extended simulation has once again denatured the
protein and the RMSd creeps up quickly.
I don't understand why the system is getting destabilized with cuda ? Can
someone comment on this issue?
Thanks,
Mani
--
Manikanthan Bhavaraju
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Received on Wed Jun 25 2014 - 15:00:02 PDT
