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

[Justin Lemkul]

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
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>>>> 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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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

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