Itamar Kass wrote:
Hi Mark,
I didn't had the time to do the SD yet, but serial run end with the same
results. I didn't try water only system, as this is of no interest to me, but I
will simplify the system later on.
Being of interest to you and being a useful diagnostic may be different. It's
important to rule out different variables to arrive at a solution, which I
suspect is of interest to you. You also haven't addressed points #1 and #6 in
Chris' message.
-Justin
Cheers,
Itamar
On 01/09/2011, at 10:51 AM, Mark Abraham wrote:
On 1/09/2011 10:20 AM, Itamar Kass wrote:
Hi Chris,
Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4
again, now starting from a 5 ns simulations run using 4.0.7, and again the
simulations had stopped after 1000 LINCS error (I can extend the simulations
using 4.0.7).
I know that gromacs stopped after 1000 LINCS, but this is usually a sign that
something bad is going on in the system.
OK. Chris suggested a number of other strategies that will help determine which
aspect of 4.5.4 is behaving differently. How did those strategies work out?
Mark
Cheers,
Itamar
On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote:
OK, here's my last few ideas:
1. Please try to repeat this with gen_vel set to the same value as your
temperature coupling
2. Can you reproduce this in serial?
3. Can you reproduce this with the sd integrator?
4. Can you reproduce this with a simpler system? protein in vacuum or just
water or remove the ions, etc?
5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under
4.5.4. Do you get the same lincs warnings?
6. Also, note that you are getting warnings and the run does not actually crash
but just stops after too many warnings. So what are atoms 981 and 982? Does
their motion look different in an important ways between the 4.0.7 and 4.5.4
trajectories?
Chris.
-- original message --
Hi Chris,
thanks for the advice, I have to say I tried this as well without any success.
Itamar
On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:
run an EM with flexible water. I often find that this is the only way to get a
stable system. 500 steps of steep with define=-DFLEXIBLE (or different
depending on your water model I think) should be enough.
Chris.
Hi Chris and Justin,
On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
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"In theory, there is no difference between theory and practice. But, in practice,
there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu
============================================
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-----
"In theory, there is no difference between theory and practice. But, in practice,
there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu
============================================
--
========================================
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
========================================
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