[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 30 14:52:03 CEST 2009
Pawan Kumar wrote:
> Respected Sir,
>
> Greetings from Pawan.
> I did the Inflategro procedure for the POPC bilayer generated using genconf.
> It took around 26 compressions for coming near the initial area (just
> above it).
> The minimization were all converged to Fmax < 1350.
> If I decrease the Fmax less than this I am getting machine precision.
> But when I proceeded with the final compressed structure for pr mdrun it
> gave lincs warnings and ended with segmentation fault.
> As an alternative to this bilayer I used the DPPC bilayer
> (pre-equilibrated) which is given in GMX-Benchmark distribution.
> I carried out the same steps of Inflategro. I used the cutoff of 14 A in
> the inflation and compression step also.
> In this case the the Steepest Descents converged to Fmax < 1000 in all
> the steps. The maximum force war never above 850.
> But when I did position restraint mdrun with the last compressed file I
> got Lincs warnings and Segementation fault after few steps (30 - 40 steps).
> Can you please help how to proceed ?
>
If the minimization procedure is adequately finishing, then the problem comes
from something you are doing. If you post your .mdp file, we may be able to see
if there are any obvious mistakes.
-Justin
> Thanking you,
>
> Yours sincerely,
> Pawan
>
>
> On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Pawan Kumar wrote:
>
>
> Respected Sir,
>
> Greetings from Pawan.
> I read in the manual about the freeze-grps but dint find a good
> explanation about the usage.
> Can you please tell me how to use freeze-grps in all dimensions
> during the minimizations ?
>
>
> If you search for "freezegrps" within the list archive (the "Search"
> feature of the Gromacs homepage), you will find several hundred
> results, many of which provide examples of what users are trying and
> what may or may not work. This should be instructive.
>
> In a general sense, freezegrps are just like anything else under the
> group theory in Gromacs. Make an index group for the group of atoms
> you want to freeze (i.e., headgroups) and the dimensions in which
> you want them frozen (x, y, z - yes(Y) or no(N) for each).
>
> If you are choosing the route of POPE, it is very difficult to get
> these systems built using InflateGRO. At least, that has been my
> experience. Prepare to spend a lot of time with trial and error and
> very careful equilibration.
>
> -Justin
>
> Thanking you,
> Pawan
>
> On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
> Pawan Kumar wrote:
>
> Respected Sir,
>
> Thanks for all your help, suggestions and guidance.
> I have few more queries.
> Which type of box is appropriate in editconf - cubic or
> triclinic ?
>
>
> That depends entirely upon the dimensions of your system and
> what is
> adequate to accommodate the size of your embedded protein.
>
>
> I have read in one of your mails in the archives that POPE
> bilayer contains some bad interactions. As it contains
> more no.
> of lipids (340) it covers the full protein ( trimer which
> I am
> working on ) other than the few loop regions. How far that
> bilayer can be used or is it fine to use the biger bilayer of
> popc128a whcih I obtained by genconf ?
>
>
> The choice of lipid should not be based on a size
> convenience. It
> should be based on a valid model system, and experimental
> evidence
> to which you can correlate your results, if possible.
>
> POPE presented a terrible challenge, since during the in vacuo
> InflateGRO minimizations, the headgroups folded in on
> themselves to
> form intra-molecule hydrogen bonds that resulted in a collapse of
> the molecule. The solution was to use freeze-grps in all
> dimensions
> during these minimizations, and then equilibrate very carefully.
>
>
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
> (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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