[gmx-users] Re: Inconsisten shift Error

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> 
> Hi Justine,
> 
> Here is the procedure I followed….
> 
> I developed my PDB structure (non-protein means it is a polymer called 
> PAP) using Material studio…. Get the PDB file and process it using the 
> PRODRG…. I got both the GRO and TOP files………. However, PRODRG gave me a 
> TOP and GRO file for a deprotonation carboxylic acid functional group, 
> so I have to modify it my self as follows.
> 

Manual hacking should not be necessary.  See the PRODRG FAQ regarding the 
ADDHYD/DELHYD commands.

> Inside the initial Topology
> 
> 44 CH1 1 UNK CA    13    0.143    13.0190
> 45 C     1 UNK C      13    0.372    12.0110
> 46 OM  1 UNK OXT  13    -0.757   15.9994
> 47 OM  1 UNK O     13    -0.758   15.9994
> 
> The modified topology
> 
> Which means I have manually modified the entire topology by including 
> the H group (HO) in the COO- functional group.... 
> =============================================
>     44       CH1     1  PAP      CA    13    0.000  13.0190
>     45         C       1  PAP       C     13    0.530  12.0110
>     46         O      1  PAP     OXT    13   -0.380  15.9994
>     47        OA     1  PAP       O      13   -0.548  15.9994
>     48        HO     1  PAP     HAA    13    0.398  1.00800
> ==============================================
> 
> So from 54 atoms now became 55 atoms and their order is also rearranged 
> …. To match the GRO file. I took the charges from the asparagines 
> residue for the carboxylic acid in the ffgmx.
> 

I assume you mean protonated aspartate, and that seems reasonable enough to do.

> I have modified the GRO file as well because the coordinated are for 54 
> but now I have included the H atom at the right position…… I visualized 
> that and it worked fine….
> 
> 
> Hence this is a new amino acid residue now as it does not exist in the 
> residue database….
> 
> I have chosen the ffgmx force field since the other force fields does 
> not allow me to go through… therefore I included this force field using
> 

Well, there has to be a reason.  You can develop parameters for any force field. 
  I'm not saying ffgmx is the root cause of your problem, but choosing a force 
field simply because it seemed to be the most convenient is a really lousy way 
to make an extremely important choice.

> ; Include forcefield parameters
> #include "ffgmx.itp"
> 
> [ moleculetype ]
> ; Name nrexcl
> PAP      3
> 
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CH3     1  PAP     CAZ     1    0.000  15.0350
>      2       CH2     1  PAP     CAK     1    0.000  14.0270
> -
> 
> -
> -
> ; Include Toluene topology
> #include "Toluene.itp"
> 
> 
> #ifdef posres

Watch your capitalization - see the note below.

> ; Position restraint for PAP
> [ position_restraints ]
> 
> #include "posres.itp"
> 
> #endif
> 
> 
> [ System ]
> ; Name
> PAP in Toluene
> 
> [ molecules ]
> ; Compound        #mols
> PAP               1
> 
> Energy minimization
> 
> grompp -v -f  minim.mdp  -c PAP.gro -p PAP.top -PAPX.tpr
> mdrun –v deffnm PAP.tpr
> 
> Now the Construction of the Box….multiple conformations … in this case 8 
> molecules
> 
> genconf –f  PAPX.grob –nbox 2 2 2 –rot  –dist 0.1 0.1 0.1 –o PAPY.gro
> 
> Followed by………………….
> 
> But I want to enlarge the whole box ………………
> 
> Editconf –f PAPY.gro –box 10 10 10 PAPZ.gro
> 
> I checked the GRO file and the volume changed from 4.3 4.3 4.3 to 10 by 
> 10 by 10
> 
> Energy minimization…………of the SYSTEM followed by SOLVATION with toluene..
> 
> 
> 
> 
> genbox –cp PAPZ.gro –cs toluene.gro –o PAPD.gro

<snip>

> Energy minimization of the system …. I just also check the distance of 
> each solvent molecule and they are not overlapped each other as the 
> –dist option is set a little big…
> 
> It converged to Potential Energy 1.362e+05
> Max force = 5.3+1
> Norm of force = 1.287
> 
> 
> For Fmax less than 100………………………It converged in 11351!
> 

I don't understand what you mean here.  Your Fmax appears to be 53, not 11351. 
If it is actually 11351, then there is a huge repulsive force somewhere in the 
system (mdrun prints the atom number).  Furthermore, your potential energy is a 
very large, positive number, indicating repulsive interactions in your system. 
This is probably the root cause of your problems.  There are some bad steric 
clashes somewhere, or the parameters for some species (either PAP or TOL) are 
unreasonable.

> I checked the volume is 1000 and density is 644 and total mol is 3435……
> 
> Now I want to relax my system…………..
> 
> Position restrain……………….. using.............. It run for long and all of 
> a sudden it crushed ….
> 
> The following error…………………………………………
> 
> 

For readability, please use some semblance of normal punctuation :)

<snip>

OK, so your system is blowing up.  See the page of the same title on the Gromacs 
site for general tips, but it probably stems from the ridiculously high 
(repulsive) potential, and perhaps the huge Fmax (which is unclear above).

Your .mdp files look reasonable enough, except that -DFLEXBILE int the em.mdp 
file really isn't doing anything if you don't have water in your system.  Of 
potential note - in your topology, you have an "#ifdef posres" statement, but 
then you use "-DPOSRES" in the pr.mdp file; I do not know if such things are 
case-sensitive, but I suspect they are.

> I need your HELP!!!!!!!!!!!!!!!!!!!! I spent lots of time trying to 
> figure out this!!!!
> 

No need to shout :)  It's very hard to figure out someone else's problem via 
email, especially over the course of several days and while in the midst of 
one's own work.

-Justin

> Rob
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> teklebrh at ualberta.ca wrote:
>>> Hi Justin,
>>>
>>> I just checked this error on the archive list but could not found a 
>>> reasonable answer ......
>>>
>>> I have done the energy minimization and it is ok Fmax less than 100
>>>
>>> but when I start equilibrating my system I got the following error..
>>>
>>> =================================================
>>> There were 2 inconsistent shifts. Check your topology
>>>
>>> Warning: 1-4 interaction between 18851 and 18856 at distance 42.558 
>>> which is larger than the 1-4 table size 1.900 nm
>>>
>>> These are ignored for the rest of the simulation
>>>
>>> This usually means your system is exploding,
>>>
>>
>> Here's the usual advice:
>>
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>
>> <snip>
>>
>>> tcoupl                   = V-rescale ; modified berendsen thermostat
>>> ; Groups to couple separately
>>> tc-grps                  = PAP TOL
>>
>> What are PAP and TOL?  Are they of sufficient size to justify their 
>> own temperature coupling groups?
>>
>> http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>> Other than that, you'll have to give some information about what your 
>> system is, how you built it, and what parameters (force field) you're 
>> using.
>>
>> -Justin
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================