From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Mar 04 2009 - 19:41:06 CST
If you are using a script as input to psfgen, can you paste the script in a
reply email? Can you also paste the namd configuration file. Sounds like
something could be wrong with angle, vdW, etc definitions in the psf or
parameters read-in during NAMD's startup.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Wed, Mar 4, 2009 at 1:36 PM, Brittany Morgan <brmorgan_at_clarku.edu> wrote: > Hi Chris, > > > > Your suggestion of using a dcdfreq of 1 worked; I found the problem but I > am not sure why it is happening. It seems to be a problem with amide > protons. In the initial structure, they are fine, but after minimization, > almost all of the amide protons are rotated so that they are inside of the > carbonyl carbon! The minimization is actually causing the problem… It > doesn’t matter if I use rigidBonds on or off during minimization. Once I > start the dynamics, some of them begin to oscillate wildly, causing the > Rattle failure. > > > > I think that something must be going wrong when I generate the psf (using > psfgen), but nothing appears wrong visually and I get no errors or warnings > of any kind. I use ‘pdbalias atom XXX H HN’ for each residue (where XXX is > the 3 letter residue code), but it reads in all of the coordinates correctly > without an issue. > > > > Any idea what might be causing this? > > > > Thanks, > > Brittany > > > ------------------------------ > > *From:* charris5_at_gmail.com [mailto:charris5_at_gmail.com] *On Behalf Of *Chris > Harrison > *Sent:* Wednesday, March 04, 2009 12:20 PM > *To:* Brittany Morgan > - Show quoted text - > *Subject:* Re: namd-l: Minimization convergence issue > - Show quoted text - > > > > Brittany, > > What is the timestep for the beginning of the MD (not minimization) and the > first Rattle failure? If first Rattle failure occurs several steps after > the beginning of the MD, try dropping your dcdfreq to 1, collecting all the > frames and then visualizing them (specifically looking at atoms near and > interacting with those atoms suffering from the Rattle failure) to see if > you notice anything obviously problematic. > > > C. > > > -- > Chris Harrison, Ph.D. > Theoretical and Computational Biophysics Group > NIH Resource for Macromolecular Modeling and Bioinformatics > Beckman Institute for Advanced Science and Technology > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 > > char_at_ks.uiuc.edu Voice: 217-244-1733 > http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar> > Fax: 217-244-6078 > > > On Mon, Mar 2, 2009 at 10:53 AM, Brittany Morgan <brmorgan_at_clarku.edu> > wrote: > > Hi Peter, > > There are no additional constraints or restraints on the system. I haven't > tried generating the psf using my old procedure, because it is very > tedious. > However, comparing the original PDB structure with my new structure in VMD > shows them to be identical (same positions, no extra bonds or atoms). The > only difference from the original PDB (NMR structure with all hydrogen > atoms > present) is that mine is solvated and ionized. > > Could it be an issue with atom names? I did a lot of aliasing with psfgen > and in the end I had no errors, warnings or spurious bonds. But, it might > be > possible to have swapped the names of two atoms without generating extra > bonds (say, two hydrogens connected to the same carbon), but if it doesn't > generate extra bonds, I fail to see how it would be an issue in the > minimization. > > > Thanks, > Brittany > > - Show quoted text - > > > > > -----Original Message----- > From: Peter Freddolino [mailto:petefred_at_ks.uiuc.edu] > Sent: Monday, March 02, 2009 11:30 AM > To: Brittany Morgan > Cc: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: Minimization convergence issue > > Hi Brittany, > are you placing any additional constraints or restraints on the system? > If you visually inspect your structure (maybe comparing the same > structure generated using your new and old procedures), does everything > look ok? Did you get any warnings from psfgen? It's odd that you'd have > difficulties with structures made by psfgen if the initial coordinates > are ok... > > Best, > Peter > > Brittany Morgan wrote: > > Hello all, > > > > > > > > I am having a problem with convergence of the minimization routine. The > > gradient tolerance convergences rapidly at first, but then fluctuates > > around 40-100 and will not continue to decrease. If I try to go ahead > > and run dynamics, even with a very conservative time step (0.5fs with a > > 1e-6 SHAKE tolerance), I get a RATTLE constraint error, but it is not > > the same atom every time. > > > > > > > > I have tried SHAKE on or off during minimization, varying the length of > > minimization from 1,000 to 20,000 steps and I also tried using the > > velocity quenching algorithm for 1,000 steps initially and then doing > > additional conjugate gradient minimization. Turning SHAKE off during > > minimization helped some (fluctuates between 10-40) for one structure at > > least, but it didn't solve the problem. > > > > > > > > I have never had this problem in the past, and now it is happening for 4 > > structures. The difference is that I am using psfgen (using a script, > > not the GUI) to generate the input files for NAMD instead of using > > CHARMM. I can't find any difference when comparing the output of psfgen > > with the original PDB files, and the structure after minimization is not > > very different from the starting state. I'd prefer not to go back to > > using CHARMM, since it is a pain comparatively for me, but I don't know > > what else to try. > > > > > > > > Any suggestions? > > > > > > > > Thanks, > > > > Brittany Morgan > > > > >
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