From: Werner Crous (crous.werner_at_gmail.com)
Date: Thu Mar 18 2010 - 04:29:55 CDT
I accidently sent the previous unfinished message. Pleas ignore this.
On Thu, Mar 18, 2010 at 11:23 AM, Werner Crous <crous.werner_at_gmail.com>wrote:
> Dear Chris
>
> Thank you for the response. I did try splitpatch and this also did not work
> and I do not really want to have flexible bonds between the heavy atoms and
> hydrogens. Since the problem, I tried to use the input coordinates of the
> file that I used to run NPT dynamics in CHARMM and this also did not work.
> The rationale behind the last step was that maybe the protein drifted a
> little in the water box in the NPT simulation. I even tried a minimization,
> but I got the same error. I am now trying to understand what causes it. I
> hope you can help me. On my Windows version of VMD the bonds to the hydrogen
> atoms of my water molecules look elongated, but on the UNIX version it does
> not. I am not sure how to fix the input coordinates so that the bonds look
> normal in VMD. Thank you in anticipation.
>
Regards
Werner
>
> On Wed, Mar 17, 2010 at 7:13 AM, Chris Harrison <charris5_at_gmail.com>wrote:
>
>> Werner,
>>
>> Please have a look at the NAMD troubleshooting guide:
>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
>>
>> Pay particularly close attention to the "Bad global exclusion count"
>> section and the suggested fix:
>>
>> -----
>> These errors generally indicate that two atoms that are (ususally
>> implicitly) excluded are on non-neighboring patches or are more than the
>> cutoff distance apart. The situation is analogous for bond, angle, dihedral,
>> or improper count errors.
>>
>> This is often caused by similar input problems as in "Atoms moving too
>> fast" above. In particular, atoms with uninitialized coordinates (0,0,0) may
>> cause this error on the first timestep.
>>
>> This will also happen if you have a periodic cell and the input
>> coordinates to NAMD are wrapped on a per-atom basis so that there are bonds
>> to hydrogen atoms extending across the cell (i.e., you load the psf and pdb
>> in VMD and see very long bonds to hydrogens). *You can work around this
>> with the ancient "splitPatch position" option, which makes every atom its
>> own hydrogen group (this option disables rigid bonds and hurts performance,
>> so don't use it normally). It's better to just fix the input coordinates so
>> that the bonds look normal in VMD. *
>>
>> Another possibility is that some atoms are specified more than once, for
>> example one residue ends up in two chains. This is very difficult to spot in
>> VMD as these duplicate atoms have the same coordinates.
>>
>> -----
>>
>> Should this fail to fix your problem, please let us know.
>>
>>
>> Chris
>>
>>
>> --
>> 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 Sat, Mar 13, 2010 at 11:22 AM, Werner Crous <crous.werner_at_gmail.com>wrote:
>>
>>> Dear NAMD-users
>>>
>>> I setup a large system in CHARMM, done minimization and 200ps NPT
>>> dynamics, with no problems. However, when I tried to continue dynamics with
>>> NVT in NAMD I got the error listed in the subject line. I read almost every
>>> account of this error on the list, and it seems to me that it has to do with
>>> the way in which NAMD partitions the system in patches and that some of the
>>> water molecules in my system, that were wrapped to the unit cell by NAMD,
>>> were "split" in the process with some atoms of the water molecules at the
>>> top and others at the bottom of the unit cell. As I understand it, NAMD
>>> cannot put molecules with "elongated bonds " longer than the cut-off
>>> distance in a patch and this causes the error. I do not understand how this
>>> could have happened since I imaged my water molecules in CHARMM by residue.
>>> Can someone please tell me if there is a quick way of fixing this and how to
>>> prevent this error form occurring in the future? I ran successful
>>> simulations with NAMD in the past and this is the first time this error
>>> occurs.
>>>
>>> Best regards
>>> --
>>> Werner Crous
>>> Scientific Computing Research Unit
>>> University of Cape Town
>>> Rondebosch 7701
>>> South Africa
>>> Phone: +27 21 650 2530 (O)
>>> Fax: +27 21 686 4333
>>> http://scru.uct.ac.za
>>> http://scientificomputing.com
>>>
>>
>>
>>
>>
>>
>
>
> --
> Werner Crous
> Scientific Computing Research Unit
> University of Cape Town
> Rondebosch 7701
> South Africa
> Phone: +27 21 650 2530 (O)
> Fax: +27 21 686 4333
> http://scru.uct.ac.za
> http://scientificomputing.com
>
-- Werner Crous Scientific Computing Research Unit University of Cape Town Rondebosch 7701 South Africa Phone: +27 21 650 2530 (O) Fax: +27 21 686 4333 http://scru.uct.ac.za http://scientificomputing.com
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