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-- B. Lachele Foley, PhD '92,'02 Assistant Research Scientist Complex Carbohydrate Research Center, UGA 706-542-0263 lfoley.ccrc.uga.edu ----- Original Message ----- From: Lachele Foley [mailto:lfoley.ccrc.uga.edu] To: amber-developers.scripps.edu Sent: Tue, 11 Nov 2008 13:27:09 -0500 Subject: Re: amber-developers: Extra Points Calculation > > We thought it does, but Lachele discovered more problems yesterday > > evening; he was going to take a look today. > > I kept having jobs fail... I could only get them to behave on 2 processors. > I hadn't even looked, graphically, at the output. Silly me. > > The minimization isn't doing quite what I expect. Load the attached > topology and restart into vmd or something and you will find, if you twirl > the system the right way, a lovely rift between two halves of the solvent, > with the sucrose molecule spanning the gap, more or less. The starting > coordinates look like a standard array of water molecules dropped around a > solvent, so this is something the minimization is doing. Also attached is > my MIN.in file in case there is some EP-relevant keyword I didn't set > properly. If I had to make a blind guess, I'd say the two processors aren't > talking to each other in quite the way they should -- like half the solvent > went to one, and half went to the other, and neither knows exactly where the > other is. Or something. > > And, for what it's worth, The CP running on two processors seems to be > slowly correcting the problem. It's over 100,000 steps and the coordinates > look pretty good now. At first, it was what you'd expect. I can send some > or all of that output if anyone wants to see it. > > :-) Lachele > -- > B. Lachele Foley, PhD '92,'02 > Assistant Research Scientist > Complex Carbohydrate Research Center, UGA > 706-542-0263 > lfoley.ccrc.uga.edu > > > ----- Original Message ----- > From: Volodymyr Babin > [mailto:vbabin.ncsu.edu] > To: amber-developers.scripps.edu > Sent: Tue, 11 Nov > 2008 07:20:07 -0500 > Subject: Re: amber-developers: Extra Points > Calculation > > > > > Does it solve Lachele's problem (the sucrose_EP test case)? > > > > We thought it does, but Lachele discovered more problems yesterday > > evening; he was going to take a look today. > > > > > As far as I can see, that example does not include any "LP" atoms, > > > and I don't think we should be expanding to that...my recollection > > > was that "LP" atoms (still found in > > > some old parameter/topology files) were *not* treated as extra points, > but > > > as real atoms. > > > > I see. Then probably the 'LP ' part is unneeded indeed. I am not a > > right person to judge here. > > > > > I tried to expand the size of max14 (not as much as you did), and was > > > still getting segfaults on Lachele's example. > > > > This is because of too short nb14_list and i14 (their sizes are > proportional > > to the max14, but max14 is not used in the corresponding allocate()). > > > > Volodymyr > > > >Received on Fri Dec 05 2008 - 14:28:29 PST