[gmx-users] Inconsistent shifts.

[Mitchell Stanton-Cook]

Hi David,

Using GMX3.2.2 unfortunately introduces more problems. See my message on 
the 10/08/2007. I recently came across a post suggesting this is due to 
a error in Reaction Field, however I believe that this problem me be a 
little deeper.

I have come across inconsistent shifts before - it corresponds to when 
the metal ion crosses a PBC. I think the conclusion I came to last time 
after some investigation was that I should not worry? Do these 
inconsistent shifts affect my simulations ? However, this time I am a 
little uncertain. Partly due -

Distance restraints were used to co-ordinate the metal ion. I also 
created a pseudo-bond between the metal ion and a single co-ordinating 
residue. This was due to what I believe to be a problem in the 
orientation restraints code. I found that when the metal crossed the PBC 
the orientation tensor "both grew and fluctuated" by large orders of 
magnitude. I concluded that this was due to PBC not being handled 
correctly. Since the introduction of the pseudo-bond there have been no 
problems. Given that the metal ion is now by definition part of the 
protein, PBC should not be an issue and I should not be seeing 
inconsistent shifts?

Cheers

Mitch



David van der Spoel wrote:
> Mitchell Stanton-Cook wrote:
>> I have performed a search of the archive, but am yet to understand 
>> the meaning of "inconsistent shifts".
>>
>> I am using GMX331.
>>
>> I am simulating a protein structure solved by NMR.
>>
>> I have performed EM, PR and run the structure out for 500ps of MD 
>> before beginning my production runs.
>>
>> I am using both distance (to restrain a metal ion to a binding site) 
>> and orientation restraints.
>>
>> At ~4.l ns I have complaints about "2 inconsistent shifts" repeatedly 
>> in my log file. It suggests I check my topology.
>>
>> I am a little confused. I have another simulation exactly same 
>> configuration except for a larger tau_t for the time averaging length 
>> , yet I have no complaints about inconsistent shifts!
>>
>> What does "inconsistent shifts" mean?
> has to do with periodic boundary conditions. check where your ion is 
> ith respect to the protein.
> anyway this should have been fixed in 3.3.2.
>
>>
>> Is there a way to fix this problem/ analyse what is happening?
>>
>>
>> Cheers
>>
>> Mitch
>>
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