mohsen ramezanpour wrote:
Dear Dr.justin
Thank you.You are right.
I did what you said.
please let me know the answer of my other question in first email:
I am doing iteration more than 26 times that you said in your tutorial.
I am in 28th step now and my area per lipid is 63 and I think it is
lowering everytimes I do iteration.
In the other words it seems it dosen't converge!!
It won't. InflateGRO does what you tell it. If you keep squishing the lipids,
it will happily create an unstable system. You have to know when to stop.
-Justin
What do you think?
Thanks in advance
On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
Yes,I know,it deleted some lipids according to inflateGRO script
in the first timethat I used perl command.
Besides:
I did iteration 25 times correctly,and no addition or doubling
was occured.
I used the same commands of 25th iteration.of course I changed
numberes from 25 to 26 in commands.
I think it is because I have compacted my lipids more than it is
required.
Over-packing your lipids will not cause your coordinate file to
magically be doubled.
my commands are as below:
after doing EM for output of 25th iteration(its output were
EM-inflate-26.*) I entered :
trjconv -f EM-inflate-26.trr -s EM-inflate-26.tpr
-o EM-inflate-26-trj.gro -pbc mol -ur compact
Here's the problem. You're converting a .trr (which presumably has
2 frames) and converting it to a multi-frame .gro file. All you
need is to fix the PBC on the final frame, i.e. the .gro file that
mdrun writes.
-Justin
perl inflategro EM-inflate-26-trj.gro 0.95
DPPC 0 system_shrink26.gro 5
area_shrink26.dat
grompp -f minim-strong.mdp -c
system_shrink26.gro -p topol.top -o
EM-inflate-27.tpr
thanks in advance for your reply
On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
mohsen ramezanpour wrote:
Dear all
I am doing Membrane -protein tutorial.
Actually I did each step carefully,I could score down my
lipids
26 times.
But there were two problems:
1-I get ~77 A for area per lipid in 26th step not 71 as
Dr.Justin has said
2-I tried to do more iteration to make closer my area per
lipid
to 71,But I get the following error:
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file
(system_shrink26.gro,
12876)
does not match topology (topol.top, 6438)
I checked and I found program has added some additional DPPC
molecules to my system!!
InflateGRO does not add lipids, it deletes them. Whatever you've
done has exactly doubled the system. You've managed to
concatenate
coordinate files or otherwise manipulate it in some
nonsensical way.
Without seeing the command you used it's impossible to say.
-Justin
Besides I get 32 A area per lipid for this step!!!
Please let me know what is the reason.
Thanks in advance
Mohsen
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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