Hi amber users,
I am from molecular biology lab and has limited knowledge regarding MD
simulation. I am hoping some of you might have a better idea on how to
pursue this problem.
What we want to do is using AMBER GPU cuda.spdp version to simulate our
protein at high temperature for as long as we can or until the protein
unfold, say 400K, in a system solvated with TIP3PBOX water molecules and
150mM NaCl in a solute to wall distance of 10A water box.
The reason we want to do this is we have all short of data including protein
stability of different clinical mutants (10 of them), and we can classify
the locations of mutations based on their experimental thermal stability. So
we would like to simulate these mutants and observe which part of the
structure has the least stability because of the mutation.
The strategy is:
1. Simulate the WT at 300K and 400K to serve as control.
2. Simulate mutants at 400K to observe the effect of mutation.
The protocol I used for 400K is as follow.
1. Minimization with protein fixed.
2. All atom minimization.
3. Equilibration to 300K with protein fixed.
4. Equilibration at 300K all atoms
5. Increase temp to 400K using 20ps time step.
6. simulation at 400K for as long as I can.
The input file at 400K is as below
&cntrl
imin=0, ntx=5, ntb=2, taup=2, ntp=1, cut=10, ntr=0, ntc=2, ntf=2, temp1=400,
temp0=400, ntt=3, gamma_ln=1, ntslim=10000000, dt=0.002, ntpr=1000,
ntwx=1000, ntwr=1000, irest=1, ioutfm=1
/
&ewald
dsum_tol=0.000001, nfft1=128,nfft2=128, nfft3=128
/
I am able to simulate some of the mutants and WT at 400K up to 30ns (my plan
is to simulate as long as I can, I have access to a cluster of S2050 GPUs),
but then I encountered the error "Could not read coords from
directory_name/file_name.rst " when I try to continue the simulation.I will
only see this error when the simulation went over 30ns, for the WT and
mutants simulations.
Is there anything wrong with my input parameters?
Any help and comments would be very much appreciated.
Andy
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 30 2010 - 21:00:02 PDT
