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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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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