Ok.Thank you very much<br><br><div class="gmail_quote">On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Dr.justin<br>
Thank you.You are right.<br>
I did what you said.<br>
<br>
please let me know the answer of my other question in first email:<br>
I am doing iteration more than 26 times that you said in your tutorial.<br>
I am in 28th step now and my area per lipid is 63 and I think it is lowering everytimes I do iteration.<br>
In the other words it seems it dosen't converge!!<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
What do you think?<br>
Thanks in advance<br>
<br></div><div><div></div><div class="h5">
On Mon, Mar 7, 2011 at 6:09 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
Dear Dr.Justin<br>
Yes,I know,it deleted some lipids according to inflateGRO script<br>
in the first timethat I used perl command.<br>
Besides:<br>
I did iteration 25 times correctly,and no addition or doubling<br>
was occured.<br>
I used the same commands of 25th iteration.of course I changed<br>
numberes from 25 to 26 in commands.<br>
I think it is because I have compacted my lipids more than it is<br>
required.<br>
<br>
<br>
Over-packing your lipids will not cause your coordinate file to<br>
magically be doubled.<br>
<br>
<br>
my commands are as below:<br>
after doing EM for output of 25th iteration(its output were<br>
EM-inflate-26.*) I entered :<br>
<br>
trjconv -f EM-inflate-26.trr -s EM-inflate-26.tpr -o EM-inflate-26-trj.gro -pbc mol -ur compact<br>
<br>
<br>
Here's the problem. You're converting a .trr (which presumably has<br>
2 frames) and converting it to a multi-frame .gro file. All you<br>
need is to fix the PBC on the final frame, i.e. the .gro file that<br>
mdrun writes.<br>
<br>
-Justin<br>
<br>
perl inflategro EM-inflate-26-trj.gro 0.95 DPPC 0 system_shrink26.gro 5 area_shrink26.dat<br>
grompp -f minim-strong.mdp -c system_shrink26.gro -p topol.top -o EM-inflate-27.tpr<br>
<br>
thanks in advance for your reply<br>
<br>
<br>
On Mon, Mar 7, 2011 at 5:42 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
Dear all<br>
<br>
I am doing Membrane -protein tutorial.<br>
Actually I did each step carefully,I could score down my<br>
lipids<br>
26 times.<br>
But there were two problems:<br>
1-I get ~77 A for area per lipid in 26th step not 71 as<br>
Dr.Justin has said<br>
2-I tried to do more iteration to make closer my area per<br>
lipid<br>
to 71,But I get the following error:<br>
Program grompp, VERSION 4.0.7<br>
Source code file: ../../../../src/kernel/grompp.c, line: 362<br>
<br>
Fatal error:<br>
number of coordinates in coordinate file<br>
(system_shrink26.gro,<br>
12876)<br>
does not match topology (topol.top, 6438)<br>
<br>
I checked and I found program has added some additional DPPC<br>
molecules to my system!!<br>
<br>
<br>
InflateGRO does not add lipids, it deletes them. Whatever you've<br>
done has exactly doubled the system. You've managed to<br>
concatenate<br>
coordinate files or otherwise manipulate it in some<br>
nonsensical way.<br>
Without seeing the command you used it's impossible to say.<br>
<br>
-Justin<br>
<br>
<br>
Besides I get 32 A area per lipid for this step!!!<br>
<br>
Please let me know what is the reason.<br>
Thanks in advance<br>
Mohsen<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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