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

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Edvin Erdtman wrote:
>> 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.
>>
> 
> Why are you using a cutoff during the compression phase?  You will 
> continue to delete lipids!  I have never had a problem if I scale up by 
> a factor of 4, with a 1.4-nm cutoff, then compress by a factor of 0.95 
> (with no cutoff).
> 
> Maybe that will make a difference?
> 
> -Justin
> 
>> 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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> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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