[gmx-users] Replicating and equilibrating DPPC 128 lipid. pdb

[Priya Das]

Dear Justin,

Thankyou for the clarification.
Do we use ediconf for making DPPC whole?

On Wed, Nov 19, 2014 at 4:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/19/14 6:16 AM, Catarina A. Carvalheda dos Santos wrote:
>
>> Priya,
>>
>> Did you perform at least one energy minimization step before that? Because
>> you should, one or several, to remove unfavorable interactions.
>>
>>
> ...and even more importantly: were the DPPC whole (or at least made whole)
> prior to replicating with genconf?  If not, no amount of energy
> minimization will likely save the structure.
>
> -Justin
>
>
>  On 19 November 2014 11:05, Priya Das <priyadas001 at gmail.com> wrote:
>>
>>  Dear Catarina,
>>>
>>> Thankyou very much for the reply.
>>> I was able to replicate the DPPC membrane structure.
>>> But while equlibration step  using the code :
>>> pbc  = xyz
>>> coulombtype =PME
>>> rcoulomb = 1.0
>>> rvdw = 1.4
>>> tcoupl = Berendsen
>>> tc-grps = System
>>> tau_t = 0.1
>>> ref_t = 325
>>> Pcoupl = Berendsen
>>> Pcoupltype = semiisotropic
>>> tau_p = 2.0 2.0
>>> compressibility = 4.5e-5 4.5e-5
>>> ref_p = 1.0 1.0
>>> constraints = all-bonds
>>>
>>> I get LINCS error message.
>>> But if i use NONE option for contsraints, i get results. Is it the right
>>> way of doing it?
>>>
>>> On Wed, Nov 19, 2014 at 4:17 PM, Catarina A. Carvalheda dos Santos <
>>> c.a.c.dossantos at dundee.ac.uk> wrote:
>>>
>>>  Hi Priya,
>>>>
>>>> You can use genconf with the option -box to replicate your box (in this
>>>> case your membrane) as many times as you want in the x,y and z
>>>>
>>> directions.
>>>
>>>> Keep in mind that -box only deals with integers (number of boxes), so
>>>> something like "-box 1.5 2.5 1" will be equivalent to "-box 2 3 1". If
>>>>
>>> the
>>>
>>>> system is too large after replication you can always do some scripting
>>>>
>>> and
>>>
>>>> "adjust" the final membrane size.
>>>>
>>>> After this, the equilibration of the new membrane has to be done as you
>>>> mentioned (you can follow the same procedure used to equilibrated the
>>>> initial 128 DPPC membrane, for example) and only then you align and
>>>>
>>> insert
>>>
>>>> your protein in the membrane. There are several tools available for this
>>>> last step, I would recommend using lambada for the protein alignment and
>>>> inflategro2 for the protein insertion (you can checkthis
>>>> <http://pubs.acs.org/doi/abs/10.1021/ci3000453> reference).
>>>>
>>>> Hope this helps.
>>>>
>>>> Regards,
>>>>
>>>> On 19 November 2014 09:35, Priya Das <priyadas001 at gmail.com> wrote:
>>>>
>>>>  I am working with a transmembrane protein (pentamer). From references i
>>>>> have chosen DPPC 128. pdb as my membrane structure. But as my protein
>>>>>
>>>> size
>>>>
>>>>> is huge , i need a larger simulation box. Therefore, i need to
>>>>>
>>>> replicate
>>>
>>>> the DPPC membrane because 4 such DPPC.pdb (128 lipids) forms a large
>>>>>
>>>> box.
>>>
>>>> After replicating the system has to be equilibrated.
>>>>> Is anyone aware of this process.
>>>>> Please reply.
>>>>>
>>>>> --
>>>>> *Let us all join hands to save our " Mother Earth"*
>>>>>
>>>>>  ------------------------------------------------------------
>>> ------------
>>>
>>>> Regards,
>>>>> Priya Das
>>>>> Research Scholar
>>>>> Dept. of Computational Biology and Bioinformatics,
>>>>> University of Kerala
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>>
>>>>
>>>>
>>>> --
>>>> Catarina A. Carvalheda
>>>>
>>>> PhD Student
>>>> Computational Biophysics Group
>>>> College of Life Sciences, University of Dundee
>>>> Dundee, DD1 5EH, Scotland, UK
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>>>
>>>
>>> --
>>> *Let us all join hands to save our " Mother Earth"*
>>> ------------------------------------------------------------------------
>>> Regards,
>>> Priya Das
>>> Research Scholar
>>> Dept. of Computational Biology and Bioinformatics,
>>> University of Kerala
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>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala