Ok.Thank you very much On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul <[email protected]> wrote:
> > > 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 >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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