[gmx-users] Error with equilibration of DPPC membrane with protein

[Edvin Erdtman]

Hi again
I don't know if you were aware of it, but I have commented some Justin's 
questions further down in the e-mail (my last e-mail wasn't only a 
thank-email). Since it took so long, and other similar discussions are 
still running I thought you have missed my comments (see below).

Now we have tried with a Calpha-P cutoff of 5 Å (i.e.  perl 
inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5 em2/area.dat), 
and position restraints on the protein, I have also merged Cl and SOL in 
the same temp group, but it does not seem to work anyway. We still get 
the LINCS warnings.

Thankful for all help!

/Edvin

Edvin Erdtman wrote:
> Hi again an Thank you for comments!
>
>
> Justin A. Lemkul wrote:
>> Edvin Erdtman wrote:
>>> Hi
>>>
>>> We have a problem of equilibrate the system with a protein within 
>>> DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have 
>>> been using their perl script inflategro.pl to insert our protein. We 
>>> used position restraints for the protein as mentioned in Methods 41 
>>> (2007) 475-488.
>>> We have tried with a scaling factor of 0,95 and 0,97, and a cut-off 
>>> value of 14 to expand the box and 0 to reduce the box (is that ok???).
>>>
>>> perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 
>>> em2/area.dat
>>>
>>> with scaling factor 0.95 23 steps were needed, and with 0,97 39 
>>> steps were followed.
>>>
>>
>> This seems reasonable.
>>
>>> When we have not used position restraints for the protein, and used 
>>> a cutoff value of 4 Å, the simulation were performed well even 
>>> without annealing.
>>>
>>
>> 4 A cutoff?  For what?  That is far too short for a lipid bilayer 
>> simulation. Or am I misunderstanding where you are applying this 4 
>> A?  Is it part of InflateGRO?
>>
> Yes that is a cut-off for the InflateGRO. cutoff of distance between 
> alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper 
> example of running the perl script). If the distance are within this 
> value, then that DPPC will be removed. I thought that this parameter 
> was used only in the diverging step with Inflategro, not when 
> compressing the system. Therefore we tried to run calculations with 
> that parameter set to 0 instead (above).
>>> We have tried to energy minimize the system with steepest descent  
>>> method in each step of decreasing the box.
>>
>> Do each of these minimizations complete satisfactorily?
>>
> Most of them converged to Fmax < 1000.
>
>>> After water soaking, we have tried with both cg and steep energy 
>>> minimizations.
>>> The problems we are facing:
>>> - All the  energy minimizations are not reaching Fmax < 1000
>>
>> How close to Fmax are you getting?  If it's still on the order of 
>> 10^3 you may be OK; if it's a lot larger then you have other problems 
>> to deal with.
>>
>
> The highest force we got (using scaling factor = 0.97) at step 33: 
> "Maximum force     =  2.6218958e+03 on atom 4591"
>
>> <snip>
>>
>>> tcoupl                   = Nose-hoover
>>> tc-grps                  = DPPC Cl SOL Protein
>>> tau_t                    = 0.1 0.1 0.1 0.1
>>> ref_t                    = 100 100 100 100
>>
>> Here is a potential problem.  Never couple solvent and ions 
>> separately.  Make an index group of these two merged species.  See here:
>>
>> http://wiki.gromacs.org/index.php/thermostats
>>
> Thank you for that advice, I will do that. But really I don't think 
> that is our main problem. We tried also without chlorine (system total 
> charge of +2), but we got the same error.
>> Another bit of general advice.  I had a very mysterious problem once 
>> where during equilibration of a DPPC bilayer my lipids were blowing 
>> apart for no apparent reason.  Upon very close inspection of the 
>> trajectory (setting nstxout = 1) I identified the initial location of 
>> the explosion.  A Cl- ion was immediately next to a phosphate oxygen 
>> (very hard to see!), and it was causing a huge force that was ripping 
>> my lipid apart.
>>
>> Just an idea, if the InflateGRO minimizations are working OK, but the 
>> solvated system with ions is not working.
>>
>> -Justin
>>
>>>
>>> Thankful for all help we can get!
>>>
>>> /Edvin and Sujith
>>>
>>
> /Edvin
>
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