Uh-huh.................. :-) ;-)
I visualized the .pdb in VMD and it seems OK. 

All right,  I will do the exercise for tonight. :-)

Thanks 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: Sunday, July 29, 2012 6:54 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up

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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