[gmx-users] Diagnosing + system blowing up

[Mark Abraham]

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.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at 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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