K. Singhal wrote:
Hi
1) I am using Amber03 forcefield.
2) In most cases Yes, but in others, implicit solvent simulations tend
to crash almost immediately (after reporting segmentation fault).
3) It generally takes less than a couple of 100 ps for the loss of the
secondary structure. A few times, I even received .gro files at the end
with all values as "nan".
Points 2 and 3 indicate that whatever simulations you're trying to perform are
simply unstable. If they don't crash immediately, they're giving meaningless
output, right?
Earlier I thought it might be a problem with equilibration, but I have
tried to run energy-minimization more than once followed by
position-restrained runs as well (to equilibrate H-atoms). But the end
result hasn't changed.
Do you get the same effects if you run a "normal" simulation on CPU and not GPU?
That information would be critical for properly diagnosing what's going on.
If it's not GPU-specific, in all likelihood whatever you're doing is incorrect
somewhere along the way.
-Justin
Thanks & Regards
Kush
-----------------------------------------------------------------------------------
*Michael Shirts:*
A few questions:
1) What force field are you using?
2) do you get the same answers with and without GPU acceleration?
3) How long does it take for secondary structure to disappear? 100's
of ps? 10's of ns?
--
Kushagra Singhal
Promovendus, Computational Chemistry
van 't Hoff Institute of Molecular Sciences
Science Park 904, room C2.119
1098 XH Amsterdam, The Netherlands
+31 205256965
Universiteit van Amsterdam
k.sing...@uva.nl <mailto:k.sing...@uva.nl>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
