On 29/07/2012 4:47 AM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
Uh-huh... there's a known initial issue with a bond between 18 and 1 and
later issues with 1-4 interaction between 5 and 1... and now you think
there is a bond from 18 to 5? This makes no sense.
However I see this pair in the [pairs] section of topology !
So I can get the result of an inappropriate bond interaction here! Correct?
Now I think it's not necessary to go through the diagnosing steps any more! :-(
What is my duty right now?!
Is this problem supposed to be fixed in the .pdb file? What's wrong with the
pdb file? What about erasing the unexpected bond interactions in topology file?
As I've said, at least one of your topology and initial coordinates
don't make sense. If you visualize the coordinates and they make sense,
then you need to go back and get a proper topology, like Justin said.
Blindly erasing interactions is ineffective. Go and design it properly,
probably from the beginning or from what Justin said. As an exercise,
get a simulation of Val with acetyl and some C-terminal capping residues
working. Then work out from that example how to define and use an .rtp
entry that is acetyl-Val. Then adapt that to formyl-Val.
Mark
Sincerely,
Shima
----- Original Message -----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Cc:
Sent: Saturday, July 28, 2012 7:15 PM
Subject: Re: [gmx-users] Diagnoding + system blowing up
On 28/07/2012 9:34 PM, Shima Arasteh wrote:
Hi all,
My system has got BLOWING UP . I followed the protocol in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below:
Step 1: If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the
resulting trajectory to see which atoms/residues/molecules become unstable
first.
I got this warning:
Warning: 1-4 interaction between 5 and 18 at distance 2.003 which is larger
than the 1-4 table size 2.000 nm
Classic symptom of blowing up, and much more so than all of the other problems
you reported. Please get in the habit of reading all the output before reaching
conclusions ;-)
Step 2: Simplify the problem:
If you have a new box of solvent, try minimizing and simulating a single
molecule to see if the instability is due to some inherent problem with the
molecule's topology or if instead there are clashes in your starting
configuration.
I got this:
Now there are 24 residues with 360 atoms
Making bonds...
Warning: Long Bond (1-18 = 0.357049 nm)
So you were ignoring warnings from pdb2gmx...? There's a lesson there -
everything you've done after ignoring that was doomed to fail. It can be right
to ignore a warning, but you should know why it is right. If your topology
defines a bond between atoms that are 0.35nm apart in your starting
configuration, then either your topology or configuration have a serious
problem.
So satisfy yourself whether there should be such a bond in the topology, or
whether the starting geometry is silly.
Step 3: Monitor various components of the system's energy using g_energy. If
an intramolecular term is spiking, that may indicate improper bonded
parameters, for example.
The improper-dihedral plot is strange. It "goes up in first picoseconds" and
then goes down slightly.
Sure, you probably have some inappropriate bond interaction, so something has
to give. The thing that looks weird is not necessarily the cause of the
problem, though...
I think there is something wrong in dihedrals which I defined in .rtp file in
the new residue. atom 18 is the H atom of formyl ( Formyl is as the N-terminus
and is connected to a Valine residue)
And atom 1 or 5 is...? Does that make sense?
Mark
Now , what do I need to do? Going to the next step of diagnosing? or no? How
can I fix the problem?
Would you mind helping me please and give me suggestions?
Thanks in advance.
Sincerely,
Shima
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