Hi,
we are running the following TI protocol using AMBER18 pmemd.cuda:
Full dual topology one step TI transformation. 2fs time step and full shake.
Common equilibration at lambda 0.5 and scalpha = scbeta = 0
1. minimization on cpu
2. heating to 300k 200ps
3. nvt 300k 200ps
4. npt (Monte Carlo) 1bar 300k 1600ps
TI with 14 lambda windows (values from chebyshev integration) and
scalpha = 0.5 scbeta=12
1. start with new velocities from common equilibration NPT 1000ps
2. production NPT 1000ps
each trajectory is segmented in a max length of 250ps and restarted.
The above protocol works without any crash for small ligands like the
lysozyme + bnz/phn but using larger systems like kinase + Imatinib
(gleevec) causes for edge lambdas (lambda > 0.8 or lambda < 0.2) the
system to crash.
Nothing in the stdout indicates a reason for the Error: an illegal
memory access was encountered launching kernel kNLSkinTest. Also
restarting the segment often recovers and runs just fine. The message
comes most of the times in the beginning of the run after a couple of
steps but not always. The Skin appears to have something to do with
the barostat and the box size.
Therefore, we also tried the berendsen barostat but this resulted
mainly in distorted ligand conformations (forming a pile of atoms in
space). There might also be a bug in the berendsen barostat when using
TI GPU code. We also tried 1fs with tishakemask for the ligand but
didn't help.
We are currently running a test with full NVT in each lambda
production window. However, if anybody can give us some insight what
is going on it would help us greatly.
Thanks,
Max
--
Maximilian Ebert, PhD | Applications Scientist
+1 (514) 393-1055 x136 | support.chemcomp.com
--
Chemical Computing Group | www.chemcomp.com <http://www.chemcomp.com> |
910-1010 Sherbrooke W., Montreal QC H3A 2R7, Canada | +1 514 393 1055
Manage Communications: www.chemcomp.com/Manage_Subscription.htm
<http://www.chemcomp.com/Manage_Subscription.htm>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 23 2018 - 08:00:04 PDT
