[gmx-users] membrane-protein tutorial
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 7 15:59:22 CET 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> 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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