Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
apt-get install avogadro http://avogadro.openmolecules.net/wiki/Distribution_Packages On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina lnzha...@gmail.com wrote: There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] drawing the plots
xmgrace gyrate.xvg On Sat, Apr 16, 2011 at 2:09 PM, Sajad Ahrari sajadahr...@yahoo.com wrote: hello dear Gromacs users i have Gromacs4.5.3 installed on suse11.1.but when i run commands like g_gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg i can't see any plot drawn. although the command is run with no error. by the way i have the package package xmgrace-5.1.21-27.91.x86_64 already installed. thanks! sajad gmx-users@gromacs.org -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation error
You are really PATIENT waiting for FOUR months for the answers. Ask the person around you they might be able to provide useful suggestions. There might be some libs linking problem. I have never tried the Cygwin, you may really try searching first before waiting. lina P.S if I were you, I would try on linux. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] make_ndx
Hi, Does the ! in make_ndx work? | and work, but seems ! not work. I met something weird, suppose I choose a C11, which is from ri 1-111. if use a C11, the atom is 111 if use a C11 ri 1-111, the atom is 111 if use a C11 ri 101-111, the atom is 5. Which is expected to be 10, so this situation is wrong. if use a C11 ri 1-100, the atom is 100, which is right. I want to know how can I use ! to exclude some group? This mistake is reproducible and I didn't figure it out (Even I examined the .gro). Thanks for any suggestion. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: make_ndx
such as residue 288 which is has C when I tried a C, it's inclusive residue 288. while tried the ri 288 a C, it showed me Group is empty. Thanks, On Sun, Mar 27, 2011 at 1:42 PM, ZHAO Lina lnzha...@gmail.com wrote: Hi, Does the ! in make_ndx work? | and work, but seems ! not work. I met something weird, suppose I choose a C11, which is from ri 1-111. if use a C11, the atom is 111 if use a C11 ri 1-111, the atom is 111 if use a C11 ri 101-111, the atom is 5. Which is expected to be 10, so this situation is wrong. if use a C11 ri 1-100, the atom is 100, which is right. I want to know how can I use ! to exclude some group? This mistake is reproducible and I didn't figure it out (Even I examined the .gro). Thanks for any suggestion. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_hbond output
s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 Here is my question, since there is already one bond formed, then why there is none pairs in 1000? On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li ljg...@yahoo.com.sg wrote: If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo -- *From:* ZHAO Lina lnzha...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, 16 March 2011 13:33:57 *Subject:* [gmx-users] Re: g_hbond output @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond output
@ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_hbond output
@ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] terminated but not completely
-cpi state.cpt -append try to add those two options at the end of your mdrun lina On Sun, Mar 13, 2011 at 5:53 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I run a simulation for 4 days. Unfortunately it terminated,but not completely,1 steps from 2 has done. Is there any way to run the continue of my files? Thanks in advance for your guidances Best Regards -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] secondary structure propensities of residues
Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? Thanks for any answers. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] select in pymol after trjconv
Hi, after added ions, I got a solv_ions.gro. I use trjconv to produce the solv_ions.pdb when I view it in pymol. I showed sequence, it like 1 2 3 4 6 ODOAOEOROHODOGOOYE But the solv_ions.pdb looks pretty regular. my problem is that, how could I choose the protein parts. I tried the select protein, resi 1-48 some waters are inclusive. Thanks for any suggestion. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] select in pymol after trjconv
On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, after added ions, I got a solv_ions.gro. I use trjconv to produce the solv_ions.pdb when I view it in pymol. I showed sequence, it like 1 2 3 4 6 ODOAOEOROHODOGOOYE But the solv_ions.pdb looks pretty regular. my problem is that, how could I choose the protein parts. I tried the select protein, resi 1-48 some waters are inclusive. Do you have a very large system? If so, PDB format can only handle a fixed number of digits in the residue and atom numbering fields, so the numbering of your waters restarts from zero. Such is the limitation when dealing with .pdb files. Kind of large. I was wrong before, the newly-produced solv_ions.pdb is not regular. Before those chains numbered in sequence. now different chains numbered from 1-48 1-48 again, former is 1-96 in .gro. If you just need to make selections in PyMOL, strip the water out of the file first. It's short, the protein part, I did it manually, but the show cartoon failed to show all, only show first 1-48. I guess I gotta modify the .pdb a little. Thanks for your answering. lina -Justin Thanks for any suggestion. lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] select in pymol after trjconv
ATOM397 N ALA48 35.480 52.940 57.920 1.00 0.00 ATOM398 H ALA48 34.740 52.570 57.360 1.00 0.00 ATOM399 CA ALA48 36.190 54.120 57.430 1.00 0.00 ATOM400 CB ALA48 35.900 55.320 58.350 1.00 0.00 ATOM401 C ALA48 37.690 53.840 57.260 1.00 0.00 ATOM402 O1 ALA48 38.120 52.590 57.580 1.00 0.00 ATOM403 O2 ALA48 38.460 54.860 56.810 1.00 0.00 ATOM404 N ASP 1 7.960 12.190 74.660 1.00 0.00 ATOM405 H1 ASP 1 8.090 11.710 75.530 1.00 0.00 ATOM406 H2 ASP 1 7.210 12.840 74.760 1.00 0.00 ATOM407 H3 ASP 1 7.730 11.520 73.950 1.00 0.00 ATOM408 CA ASP 1 9.190 12.900 74.290 1.00 0.00 ATOM409 CB ASP 1 10.390 11.940 74.180 1.00 0.00 ATOM410 CG ASP 1 10.860 11.380 75.510 1.00 0.00 ATOM411 OD1 ASP 1 10.420 11.850 76.560 1.00 0.00 ATOM412 OD2 ASP 1 11.880 10.480 75.450 1.00 0.00 ATOM413 C ASP 1 9.000 13.630 72.970 1.00 0.00 ATOM414 O ASP 1 8.580 13.010 71.990 1.00 0.00 I'm guessing you have different chain identifiers, i.e. identical chains, just labeled A and B or something? I got four chains. and the .pdb from trjconv do not distinguish those things and don't show chain info. Do you have some nice way to view .gro in pymol. (compare VMD I am a bit familiar with pymol) Thanks again, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] select in pymol after trjconv
On Mon, Mar 7, 2011 at 10:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: I'm guessing you have different chain identifiers, i.e. identical chains, just labeled A and B or something? I got four chains. and the .pdb from trjconv do not distinguish those things and don't show chain info. Do you have some nice way to view .gro in pymol. (compare VMD I am a bit familiar with pymol) Renumber using genconf. You should be able to select consecutive residues in this way. Otherwise, use a couple quick text editor tricks to write in chain identifiers to make selection easy. genconf works so perfect here. Thanks again! lina -Justin Thanks again, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] where does the gromacs looks for the top data file.
Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin ~/lib and ~/share are under my home directory. the general setting (in .bash_profile) can deal with executables (PATH) and libraries (LD_LIBRARY_PATH). How can I set up gromacs looking for top data files in ~/share After in topol.top I put ; Include forcefield parameters #include /home/lina/share/gromacs/top/gromos43a1.ff/forcefield.itp I still have following problems. Program grompp, VERSION 4.5.3 Source code file: futil.c, line: 897 Fatal error: Library file residuetypes.dat not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where does the gromacs looks for the top data file.
On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin ~/lib and ~/share are under my home directory. the general setting (in .bash_profile) can deal with executables (PATH) and libraries (LD_LIBRARY_PATH). How can I set up gromacs looking for top data files in ~/share After in topol.top I put ; Include forcefield parameters #include /home/lina/share/gromacs/top/gromos43a1.ff/forcefield.itp I still have following problems. Program grompp, VERSION 4.5.3 Source code file: futil.c, line: 897 Fatal error: Library file residuetypes.dat not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Gromacs searches first in the working directory, then in $GMXLIB, then in any other directories included in the .mdp file include = -I/whatever/directory. Presumably, if you installed everything in /home/lina/, then you can source GMXRC in ~/bin and the environment will be configured for you. $ source GMXRC -bash: /home/lina/bin/GMXRC.bash: No such file or directory [lina@pineapple scripts]$ pwd /home/lina/src/build/gromacs-4.5.3/scripts I'm confused. I have no problem with what under ~/bin and ~/lib but something wrong with the ~/share. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
clean reinstallation. make uninstall make distclean rm -r the untar one from source re-install it again. lina On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.comwrote: Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one, I just ran the whole process again starting from fftw$./configure. I am not sure if that is all right, I just did it to find out the problem. In the third attempt (without issuing --enable-shared anywher), I again over-wrote the gromacs installation files, and this went well. It worked, but I don't know why? Best, Majid -- *From:* ZHAO Lina lnzha...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Mon, February 14, 2011 8:04:38 PM *Subject:* Re: [gmx-users] Gromacs Installation You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] find the relevant structure out
I do not know how to extract some special frames out (professionally), so I just simply use vim to take the relevant models out and put into a new pdb file. Are there some good ways to extract one or two frames at the end of those whole frames? Base on your answering, now I start to suspect I might make something wrong cause I did it really clumsily. Thanks for your answering, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Wednesday, November 24, 2010 3:19 PM To: Discussion list for GROMACS users Subject: Re: RE: [gmx-users] find the relevant structure out - Original Message - From: #ZHAO LINA# zhao0...@e.ntu.edu.sg Date: Wednesday, November 24, 2010 17:52 Subject: RE: [gmx-users] find the relevant structure out To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, Thanks for your answering. Due to the difference in assignment, so I wonder which one I should build a bit much more faith on? I read (by eyes) the ss.xpm produced by do_dssp, and find the relevant resi out which showed as beta-sheet, but in pymol, it's really so standard alpha-helix, when I tried alter in pymol to show the beat-sheet as the way Justine mentioned in early email, it's really look weird. It's rather more likely that you're comparing two different (parts of) structures, than one secondary structure algorithm assigns sheet and one assigns helix to the same part of the same structure. Is the residue/atom numbering consistent. What does do_dssp say about the frame you cut out to give to pymol? Mark I noticed lots of paper they use DSSP to say something. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, November 24, 2010 1:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] find the relevant structure out Hi, Visualization software can sometimes assign the secondary structure incorrectly. There has been an interesting discussion on this on the Pymol user list years ago (http://www.mail-archive.com/pymol- us...@lists.sourceforge.net/msg01574.html).Secondary structure assignment is foremost human defined. You can use different metrics to obtain assignments, and should be careful to take any one of them as 'correct'. For instance, it makes a difference whether you assign three types (helical, sheet, loop), as Pymol does, or like seven types, as DSSP does. In pymol you can set the secondary structure type manually, but I find that the internal command 'dss' usually does a good job. Note that it only works on one frame and then uses the assignment for that frame on all of them, although there may be a workaround (I'll check; something with discrete_states). The frame to use for the assignment can be given to the 'dss' command through the argument state=N, where N is the frame number. If dss doesn't give the assignment you want, you can also try 'util.ss' that uses a different metric. Hope it helps, Tsjerk On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) Mark 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar
RE: [gmx-users] find the relevant structure out
Hi, Thanks for your answering. Due to the difference in assignment, so I wonder which one I should build a bit much more faith on? I read (by eyes) the ss.xpm produced by do_dssp, and find the relevant resi out which showed as beta-sheet, but in pymol, it's really so standard alpha-helix, when I tried alter in pymol to show the beat-sheet as the way Justine mentioned in early email, it's really look weird. I noticed lots of paper they use DSSP to say something. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, November 24, 2010 1:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] find the relevant structure out Hi, Visualization software can sometimes assign the secondary structure incorrectly. There has been an interesting discussion on this on the Pymol user list years ago (http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg01574.html). Secondary structure assignment is foremost human defined. You can use different metrics to obtain assignments, and should be careful to take any one of them as 'correct'. For instance, it makes a difference whether you assign three types (helical, sheet, loop), as Pymol does, or like seven types, as DSSP does. In pymol you can set the secondary structure type manually, but I find that the internal command 'dss' usually does a good job. Note that it only works on one frame and then uses the assignment for that frame on all of them, although there may be a workaround (I'll check; something with discrete_states). The frame to use for the assignment can be given to the 'dss' command through the argument state=N, where N is the frame number. If dss doesn't give the assignment you want, you can also try 'util.ss' that uses a different metric. Hope it helps, Tsjerk On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) Mark 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield
I just tried the same way as using NA+, by genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname CL- -np Number_of_K It works, u may do a try. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Jignesh Patel [jbp...@gmail.com] Sent: Monday, November 22, 2010 3:57 PM To: gromacs user Subject: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield Dear all, Can anybody tell me how to incorporate potassium ion parameters in GROMACS for GROMOS53a6 forcefield. Thanking you in anticipation. With regards, Jignesh -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield
When I went a bit further, I found it's wrong. Sorry. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Monday, November 22, 2010 4:50 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield I just tried the same way as using NA+, by genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname CL- -np Number_of_K It works, u may do a try. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Jignesh Patel [jbp...@gmail.com] Sent: Monday, November 22, 2010 3:57 PM To: gromacs user Subject: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield Dear all, Can anybody tell me how to incorporate potassium ion parameters in GROMACS for GROMOS53a6 forcefield. Thanking you in anticipation. With regards, Jignesh -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] find the relevant structure out
I really do not know how to get those beta-sheet structures out, or maybe by which ways? Any clues are warmly welcomed and appreciated. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Sunday, November 21, 2010 11:58 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] find the relevant structure out On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] find the relevant structure out
Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] find the relevant structure out
do_dssp -f traj.xtc -s topol.tpr -o ss.xpm trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump Took several frames, here, such as model 1000, model 3000 and model 5000, and named as 1000.pbd, 3000.pdb and 5000.pdb pymol 3000.pdb intra_fit protein and (name c,n,ca) show cartoon all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. what are those files I should have looked for, and how could I find a better way to show those beta-sheet out? Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Sunday, November 21, 2010 11:58 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] find the relevant structure out On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] noxvgr
Hi, Suppose when I use gyrate, I want the output to be the eps, when I tried -noxvgr -w sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] noxvgr
I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use -xvg none in the command line. If you just want an .eps output file of the plot, use the normal XmGrace formatting (leave the command line -xvg alone) and save the output in that format. XmGrace should be capable of saving an .eps, and if not, you can take whatever image file format it gives you into Gimp and convert it. -Justin sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] noxvgr
It works (cool). Thanks for both of you. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Exporting to different formats is not done with Save As but rather Print (using Print Setup to choose the proper format). Simply saving your plot creates an XmGrace file that only it can load. -Justin Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use -xvg none in the command line. If you just want an .eps output file of the plot, use the normal XmGrace formatting (leave the command line -xvg alone) and save the output in that format. XmGrace should be capable of saving an .eps, and if not, you can take whatever image file format it gives you into Gimp and convert it. -Justin sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] DSSP error
http://biskit.pasteur.fr/install/applications/dssp http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp HTH, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@gmail.com] Sent: Wednesday, November 10, 2010 10:02 PM To: Discussion list for GROMACS users Subject: [gmx-users] DSSP error Hi, I installed in /usr/local/bin the DSSP program. And I set the environment variable with a command such as “export DSSP=/usr/local/bin/dssp”. a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc ... Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /usr/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dduigjCp to ./#dduigjCp.1# --- Program do_dssp, VERSION 4.0.5 Source code file: ../../../../src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR /dev/null 2 /dev/null --- Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] which force file has parameters for creatine md simulations
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Olga Ivchenko [olga.ivche...@gmail.com] Sent: Friday, November 05, 2010 6:02 PM To: gmx-users@gromacs.org Subject: [gmx-users] which force file has parameters for creatine md simulations Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcefield for simulations? I have attached pdb file. Thanks in advance, Olga -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dssp
Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Thanks for any advice, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] dssp
Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] dssp
I did choose 1 protein when it asked me to choose. Thanks for your answering, I may try on my desktop another time. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Linus Östberg [bio...@talavis.eu] Sent: Friday, November 05, 2010 9:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] dssp
Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] dssp
But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax /dev/null 2 /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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
RE: [gmx-users] dssp
Last email the paths really look messy, because as I said before, I modified by mine hand before posted it. Sorry about that. I did export the path before. :-) Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax /dev/null 2 /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. I still think you're setting your DSSP environment variable wrong. Please consult the link I posted before - you have to point DSSP to the *actual executable* not the directory that contains it, i.e.: WRONG: export DSSP=/opt/bin RIGHT: export DSSP=/opt/bin/dssp -Justin Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mirror reflection
Hi, which can help to get the mirror reflection of a known protein? Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] mirror reflection
Cool, but what if the mirror was set on y=-x in the x-y plane. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, October 26, 2010 8:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mirror reflection editconf -scale -1 -1 -1 On Tue, Oct 26, 2010 at 12:56 PM, Erik Marklund er...@xray.bmc.uu.se wrote: #ZHAO LINA# skrev 2010-10-26 11.46: Hi, which can help to get the mirror reflection of a known protein? Thanks, lina If it's just one conformation, then I'd just write a script that multiplies all x-, y- or z-coordinates by -1 in a pdb- or gro-file. Is that what you're after, or is it something more intricate? Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] mirror reflection
I got. -rotate. sorry and thanks. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Tuesday, October 26, 2010 8:47 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] mirror reflection Cool, but what if the mirror was set on y=-x in the x-y plane. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, October 26, 2010 8:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mirror reflection editconf -scale -1 -1 -1 On Tue, Oct 26, 2010 at 12:56 PM, Erik Marklund er...@xray.bmc.uu.se wrote: #ZHAO LINA# skrev 2010-10-26 11.46: Hi, which can help to get the mirror reflection of a known protein? Thanks, lina If it's just one conformation, then I'd just write a script that multiplies all x-, y- or z-coordinates by -1 in a pdb- or gro-file. Is that what you're after, or is it something more intricate? Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re: published paper related to protein simulation, using gromacs
Hi, I think, started from some gromacs tutorial is a nice ideas and then during those process you certainly will meet some paper. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Schlesier [schl...@uni-mainz.de] Sent: Thursday, October 21, 2010 7:45 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: published paper related to protein simulation, using gromacs Hi, use ISI Web of Knowledge or scholar.google, search for 'protein + gromacs' and you should get tons of results. Greetings Thomas Date: Thu, 21 Oct 2010 13:29:11 +0300 From: ahmet y?ld?r?mahmedo...@gmail.com Subject: [gmx-users] published paper related to protein simulation using gromacs To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID: aanlkti=wwppktarpbis1mwxg7z-queo+bqj0tfq+n...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Gromacs users, I am new user Gromacs. I want to study on protein simulation using gromacs. If possible, Can you send a few articles on the protein simulation using Gromacs?For example, I downloaded from Protein Data Base the PDB extension file of any protein. What is the purpose of protein simulation?What is commonly the forcefied used for protein simulation? Which parameters are calculated?... To answer these questions, I need the articles/papers written in this area. I will be happy if you help Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position_restraints
Hi, Fatal error: [ file protein.itp, line 9 ]: Atom index (5) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. Thanks for any clue. The part belongs to the one I want to restraints. I mean, the molecule is right. Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Intrinsically disordered proteins
Hi, 1. For those intrinsically disordered proteins, the sequence is known, how the simulations will be set up, I mean, the first PDB will be needed, how to get this one? (Ideally, not necessarily to be practical) 2. suppose I got a PDB, there were several models there, let's say 16, is it acceptable to just take one, say model 1? Thanks for any answering, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Intrinsically disordered proteins
Hi, 1. Thanks for the webpage you provided, I noticed there is a avogadro there, and right now coincidently I have a question relevant to the avogadro, When I tried the avogadro-packmol-extensions, I had installed the avogadro and packmol well, but I do not know where the avogadro plugins/modules can be put ? I tried the put the packmolextension.so under usr/lib/avogadro/1_0/extensions/ but seems not work, Might someone has tried and knew the answer, actually I had asked on the other place, but none feedback. 2. Wow, it's going to be lots of works. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, October 18, 2010 9:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Intrinsically disordered proteins #ZHAO LINA# wrote: Hi, 1. For those intrinsically disordered proteins, the sequence is known, how the simulations will be set up, I mean, the first PDB will be needed, how to get this one? (Ideally, not necessarily to be practical) http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources 2. suppose I got a PDB, there were several models there, let's say 16, is it acceptable to just take one, say model 1? Making an arbitrary choice is not a good idea. You have to justify that the model you selected is in some way representative of the ensemble. You could do that by demonstrating that your simulation overlapped the configuration space of the ensemble in the PDB file, i.e. sampled all the expected configurations, thus the starting structure was not an inappropriate bias. -Justin Thanks for any answering, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How can I best setup the nodes number
Hi, Estimate for the relative computational load of the PME mesh part: 0.33 How do I set how many nodes I should use? #PBS -l nodes=12:ppn=4 What if the PME mesh part has different values? is it okay? Before I did those kind of very blindly, just based on the most nodes I can use to hopefully run quickly. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] How can I best setup the nodes number
I think I know how many ppn one nodes have. :-) My question was that the number of ppn has something to do with the PME mesh part number or not? Why sometimes I had a big load imbalance. Thanks and best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of vinothkumar mohanakrishnan [kmvin...@gmail.com] Sent: Wednesday, October 06, 2010 4:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How can I best setup the nodes number I think the PME mesh part is ok and it should be less than 0.5 always. Regarding the nodes ask your administrator how many ppn one node have. example suppose if one node has 6 ppn then 12 nodes will have 72ppn which is sufficient to run md. hope the above explanation helps you. Regards Vinoth On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sgmailto:zhao0...@e.ntu.edu.sg wrote: Hi, Estimate for the relative computational load of the PME mesh part: 0.33 How do I set how many nodes I should use? #PBS -l nodes=12:ppn=4 What if the PME mesh part has different values? is it okay? Before I did those kind of very blindly, just based on the most nodes I can use to hopefully run quickly. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re : installation of gromacs in windows on cygwin
sudo apt-get install grace From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, October 06, 2010 11:29 AM To: Gromacs Users' List Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin bharat gupta wrote: thanks for ur help.. I have figured out the problem and not installation is going on .. I want to know one more thing that xmgrace which is required for plotting the data .. how can we install it as I have searched on google .. but I am not able to get the correct link The first Google result for xmgrace is the site you want, I don't know what else to tell you. http://plasma-gate.weizmann.ac.il/Grace/ Follow whatever documentation they provide to install it. -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] protein embedded into membrane.
Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I noticed some warnings like this: Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) when I removed those residues such as 491 (none), not protein ones, those warning disappeared. I noticed on Justine's tutorial, there were 26 iterations of scaling down. I did those iterations step by step manually before and cost me nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 hours or more to write a short and clumsy script to save mine 40 mins work in the future. This is not the point. The point was that, are there some shortcuts? I wonder whether I could avoid doing those inflategro first, and then shrink and energy minimization also being avoided by simply removed those lipids (I know I still need a final EM). or, Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. How could I make sure the removal ones are going to be nice, from which sides I should check. Thanks and best regards, lina p.s To avoid a very trivial description, I put some background information below, thanks for your time. from Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis and Justine's webpage http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I tried pack the lipids around the protein, no doubt followed perfectly based on the tutorial before. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] protein embedded into membrane.
Thanks for your answering. I will check those further later. The unclear question was that, to the final .gro. How can I tell it that one (protein embedded in membrane) is okay or nice, so I can continue. based on area per lipids, or after EM ... are there some criteria? Thanks and best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, October 04, 2010 11:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein embedded into membrane. #ZHAO LINA# wrote: Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I noticed some warnings like this: Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) when I removed those residues such as 491 (none), not protein ones, those warning disappeared. VMD is detecting close contacts, not actual bonds, but since its heuristic algorithm tells it there are bonds, then you get these warnings. Perhaps a simple EM will resolve them, but maybe not. I noticed on Justine's tutorial, there were 26 iterations of scaling down. I did those iterations step by step manually before and cost me nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 hours or more to write a short and clumsy script to save mine 40 mins work in the future. This is not the point. The point was that, are there some shortcuts? I wonder whether I could avoid doing those inflategro first, and then shrink and energy minimization also being avoided by simply removed those lipids (I know I still need a final EM). or, What is presented in the tutorial is simply one way to build a membrane protein system. If you have an easier case, then as long as you can justify your methods, do what you see fit. Perhaps the iterations of InflateGRO are, in your case, unnecessary. There is also a new tool called g_membed that might be useful. It is far more automated than InflateGRO, but I have never used it myself. Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. Not to my knowledge, unless you write this program yourself. How could I make sure the removal ones are going to be nice, from which sides I should check. I don't understand what you're asking for here. -Justin Thanks and best regards, lina p.s To avoid a very trivial description, I put some background information below, thanks for your time. from Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis and Justine's webpage http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I tried pack the lipids around the protein, no doubt followed perfectly based on the tutorial before. -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] cholesterol
Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. Thanks with best regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] cholesterol
Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] cholesterol
Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] cholesterol
Thanks for your clue. I found the very interesting paper about that force field. Thanks again, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Piggot [t.pig...@soton.ac.uk] Sent: Friday, October 01, 2010 9:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org
[gmx-users] lipids number
Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those coordinates easily from those dppc128 ones. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] lipids number
I have a vague impression about that, seems someone asked similar things before. I will do a try and see. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 29, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipids number #ZHAO LINA# wrote: Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those coordinates easily from those dppc128 ones. You can make integer multiples of a box with genconf -nbox. Otherwise use genbox -cs dppc128.pdb -box (x y z) until you get a system of appropriate size. There was a very similar post yesterday about this same topic. I would suggest you have a look at the information Chris Neale posted about the specifics of box size (genbox caveats) and the need for proper equilibration. -Justin Thanks and best regards, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Getting started - Peptide
Are you sure you installed the version 4.0.7? Hint : your program run on VERSION 4.5.1, Answer : You know. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Artur Panczakiewicz [apanczakiew...@gmail.com] Sent: Thursday, September 23, 2010 10:02 PM To: gmx-users@gromacs.org Subject: [gmx-users] Getting started - Peptide Dear Gromacs Users, I'm a freshman and would like to lear how to use GROMACS in my research starting from tutorial. I've just installed the newest version and try to repeat all of the steps from the chapter that describes the preparation of Ribonuclease A to MD simulation. In my case it is not possible, unfortunatelly. The grompp program crashes such a way: --- Program grompp, VERSION 4.5.1 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried to install GROMACS on other machine with different Linux distribution but the error in grompp was the same. What is important, I installed version 4.0.7 and it works well! I don't have any idea what is going on. Does anyone have a similar problem? Regards, Artur -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position Restraints
Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. Thanks with regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Position Restraints
Thanks for your answer. How can I tell which ones I should restrain? all no-H atoms? in most general situations. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:15 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. The answer depends on your needs. When running genrestr without an index file, you can choose from any of the default groups. If you provide an index file, any group can be chosen. The default behavior of pdb2gmx is to generate a posre.itp file that restrains all heavy (non-H) atoms. You can do the same with genrestr if you want, but again, the atoms you want to restrain depend on your goals. -Justin Thanks with regards, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Position Restraints
Thanks for your answer again. I will restrain the heavy atoms only first. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:43 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: Thanks for your answer. How can I tell which ones I should restrain? all no-H atoms? in most general situations. For the sake of clarity in the archive, it's probably best to avoid broad generalizations. People can easily stumble upon a post and take it way out of context. A general situation might encompass a lot. I will reiterate that if you want to recapitulate the behavior of pdb2gmx with respect to typical biomolecules, you should choose all non-H atoms. If you have some other specialized application, I can make no recommendation, nor can anyone else, in the absence of a more thorough description. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:15 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. The answer depends on your needs. When running genrestr without an index file, you can choose from any of the default groups. If you provide an index file, any group can be chosen. The default behavior of pdb2gmx is to generate a posre.itp file that restrains all heavy (non-H) atoms. You can do the same with genrestr if you want, but again, the atoms you want to restrain depend on your goals. -Justin Thanks with regards, lina -- 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] top directory can be split or not?
Hi, Just curious, whether the top directory can be split like: /usr/share/gromacs/top /usr/local/share/gromacs/top $HOME/share/gromacs/top Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to let the grompp finding library from working directory first.
Hi, The HO atom type was in the working directory .itp file. How can I let the grompp work from searching the library of the working directory, not like this: grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 165 of the 1596 non-bonded parameter combinations --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype HO not found --- Do I need add something in minim.mdp? Or maybe just some parts wrong I do not realise. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] how to let the grompp finding library from workingdirectory first.
Yes. I did it already. But it did not work. in topol.top file, ;Include topology #include HO.itp Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Tuesday, September 14, 2010 12:48 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] how to let the grompp finding library from workingdirectory first. What is the contents of your topol.top and HO.itp file? Does the topol.top “include” the HO.itp in it? To have an “included topology file” (.itp) file processed by grompp, it has to be directed to it. This is typically done by using a #include “HO.itp” line within the topol.top file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 14 September 2010 2:33 PM To: Discussion list for GROMACS users Subject: [gmx-users] how to let the grompp finding library from workingdirectory first. Hi, The HO atom type was in the working directory .itp file. How can I let the grompp work from searching the library of the working directory, not like this: grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 165 of the 1596 non-bonded parameter combinations --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype HO not found --- Do I need add something in minim.mdp? Or maybe just some parts wrong I do not realise. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first.
The HO.itp is nothing wrong with this. I found the answer from last part of this page (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html). It's a bit trivial and I will test it later. Thanks again for you time. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Tuesday, September 14, 2010 1:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first. What is the contents of the HO.itp file? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 14 September 2010 2:53 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first. Yes. I did it already. But it did not work. in topol.top file, ;Include topology #include HO.itp Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Tuesday, September 14, 2010 12:48 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] how to let the grompp finding library from workingdirectory first. What is the contents of your topol.top and HO.itp file? Does the topol.top “include” the HO.itp in it? To have an “included topology file” (.itp) file processed by grompp, it has to be directed to it. This is typically done by using a #include “HO.itp” line within the topol.top file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 14 September 2010 2:33 PM To: Discussion list for GROMACS users Subject: [gmx-users] how to let the grompp finding library from workingdirectory first. Hi, The HO atom type was in the working directory .itp file. How can I let the grompp work from searching the library of the working directory, not like this: grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 165 of the 1596 non-bonded parameter combinations --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype HO not found --- Do I need add something in minim.mdp? Or maybe just some parts wrong I do not realise. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Need help!!!
Make sure your gromacs is the latest version. If not, update and try again. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] Sent: Thursday, September 02, 2010 9:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] Need help!!! Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tphttp://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Need help!!!
But it's a bit trivial to modify those things if you just following those steps by steps. Using the latest version can save lots of works. By the way, thanks for the website, I once followed that too (nearly step by step also). Thanks with best regards, lina P.S actually you can upgrade your website also. ^_^ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, September 02, 2010 9:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Need help!!! #ZHAO LINA# wrote: Make sure your gromacs is the latest version. If not, update and try again. The tutorial is specifically written for version 4.0.5, but will be compatible with any version 4.5. Since the re-organization of the force field directories, the information provided in the tutorial is not correct. I would recommend not upgrading until the OP has sorted out the problem and can then (maybe) work out the appropriate translation to the version 4.5.x scheme. -Justin *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] *Sent:* Thursday, September 02, 2010 9:06 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Need help!!! Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp http://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_covar
YourSourceCode/gromacs/src/tools/ If in Linux OS, try locate g_covar.c p.s 4.0.3 is not the latest version. why do not try the latest version? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carla Jamous [carlajam...@gmail.com] Sent: Monday, August 30, 2010 8:53 PM To: Discussion list for GROMACS users Subject: [gmx-users] g_covar Hi everyone, please I'm using gromacs 4.0.3, and I want to see the program g_covar, except that I have it in binary file and I want to see the C program in text format. Please how can I have access to it? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How to calculate the distances
Dear Mark, It works. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, August 26, 2010 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to calculate the distances - Original Message - From: #ZHAO LINA# zhao0...@e.ntu.edu.sg Date: Thursday, August 26, 2010 15:17 Subject: [gmx-users] How to calculate the distances To: gmx-users@gromacs.org gmx-users@gromacs.org Hi all, I guess the question I'm going to ask probably is a bit simple to those who know, well. After MD, I got a dimer, how could I get the distance of those two proteins, the centre of mass distance. In this simulation, there were six involved, but I only want to calculate the two of them. Probably g_dist. See section 7.4 of the manual for some clues, and then the man pages of the individual tools for more information. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate the distances
Hi all, I guess the question I'm going to ask probably is a bit simple to those who know, well. After MD, I got a dimer, how could I get the distance of those two proteins, the centre of mass distance. In this simulation, there were six involved, but I only want to calculate the two of them. Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the mdrun choked or maybe braked.
Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge group borders and 43271 shake borders There are 43271 total borders Division over nodes in atoms: 9348934893489351934893519348935193489351 9348935193489350 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 3245, targetcg=25208, myshift=8 CPU= 1, lastcg= 6361, targetcg=28324, myshift=8 CPU= 2, lastcg= 9477, targetcg=31440, myshift=8 CPU= 3, lastcg=12594, targetcg=34557, myshift=8 CPU= 4, lastcg=15710, targetcg=37673, myshift=8 CPU= 5, lastcg=18827, targetcg=40790, myshift=8 CPU= 6, lastcg=21943, targetcg=43906, myshift=7 CPU= 7, lastcg=25060, targetcg= 3098, myshift=7 CPU= 8, lastcg=28176, targetcg= 6214, myshift=7 CPU= 9, lastcg=31293, targetcg= 9331, myshift=7 CPU= 10, lastcg=34409, targetcg=12447, myshift=7 CPU= 11, lastcg=37526, targetcg=15564, myshift=7 CPU= 12, lastcg=40642, targetcg=18680, myshift=7 CPU= 13, lastcg=43924, targetcg=21962, myshift=8 pd-shift = 8, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 8 910 111213 G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0 0 0 0 PDIHS 774 0 0 0 0 0 0 0 0 0 0 0 0 0 IDIHS 852 0 0 0 0 0 0 0 0 0 0 0 0 0 LJ14 2436 0 0 0 0 0 0 0 0 0 0 0 0 0 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 3116 3116 3117 3116 3117 3116 3117 3116 3117 3116 3117 3116 3034 Workload division nnodes: 14 pd-shift:8 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 40643 3282 Max number of connections per atom is 27 Total number of connections is 32076 Max number of graph edges per atom is 4 Total number of graph edges is 13572 Initial temperature: 303.113 K Started mdrun on node 0 Fri Aug 13 14:38:46 2010 Step Time Lambda 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+01 Cons. rmsd () 2.63140e-05 Nothing more at the end, I changed the 16 cores to 14 cores, still has the same problem. And when I checked the status, it showed me it's finished. Thanks for any advice, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the mdrun choked or maybe braked.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, August 13, 2010 7:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdrun choked or maybe braked. #ZHAO LINA# wrote: Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge group borders and 43271 shake borders There are 43271 total borders Division over nodes in atoms: 93489348934893519348935193489351 93489351 9348935193489350 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 3245, targetcg=25208, myshift=8 CPU= 1, lastcg= 6361, targetcg=28324, myshift=8 CPU= 2, lastcg= 9477, targetcg=31440, myshift=8 CPU= 3, lastcg=12594, targetcg=34557, myshift=8 CPU= 4, lastcg=15710, targetcg=37673, myshift=8 CPU= 5, lastcg=18827, targetcg=40790, myshift=8 CPU= 6, lastcg=21943, targetcg=43906, myshift=7 CPU= 7, lastcg=25060, targetcg= 3098, myshift=7 CPU= 8, lastcg=28176, targetcg= 6214, myshift=7 CPU= 9, lastcg=31293, targetcg= 9331, myshift=7 CPU= 10, lastcg=34409, targetcg=12447, myshift=7 CPU= 11, lastcg=37526, targetcg=15564, myshift=7 CPU= 12, lastcg=40642, targetcg=18680, myshift=7 CPU= 13, lastcg=43924, targetcg=21962, myshift=8 pd-shift = 8, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 8 910 111213 G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0 0 0 0 PDIHS 774 0 0 0 0 0 0 0 0 0 0 0 0 0 IDIHS 852 0 0 0 0 0 0 0 0 0 0 0 0 0 LJ14 2436 0 0 0 0 0 0 0 0 0 0 0 0 0 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 3116 3116 3117 3116 3117 3116 3117 3116 3117 3116 3117 3116 3034 Workload division nnodes: 14 pd-shift:8 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 40643 3282 Max number of connections per atom is 27 Total number of connections is 32076 Max number of graph edges per atom is 4 Total number of graph edges is 13572 Initial temperature: 303.113 K Started mdrun on node 0 Fri Aug 13 14:38:46 2010 Step Time Lambda 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+01 Cons. rmsd () 2.63140e-05 Nothing more at the end, I changed the 16 cores to 14 cores, still has the same problem. And when I checked the status, it showed me it's finished. Please provide more information. It mdrun stopped, it must have had a reason. Please provide your .mdp file, description of the system, and what you did as far as energy minimization and/or equilibration prior to whatever this run was doing. If mdrun fails, there's always a reason, and it would be very odd if Gromacs simply stopped without providing some kind of indicative output. -Justin Can you tell me the possible reasons? Mainly which part I need to check? Thanks, lina -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use
RE: [gmx-users] Re: dimer simulation
Try to maximize the intra- and inter-peptide hydrophobic interactions? I guess it can share the same parameters, just guess, no much idea. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Vitaly Chaban [vvcha...@gmail.com] Sent: Wednesday, August 11, 2010 1:37 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: dimer simulation I think your choice should depend on what bonds you expect between the two monomers forming a dimer. -- Dr. Vitaly Chaban Dear gmx-users I want to simulate a protein which biological function defined by dimer formation. I need to simulate this protein in dimer as well as in monomeric form to solve my objectives. I am using Gromacs-4.0.4 for simulation. I have a doubt, is there any specific parameters for dimer simulation or we have to use similar parameters like monomer protein simulation. I read some literature's on dimer simulation but they are using similar parameters like monomer. -- Regards Sanjay Kumar Upadhyay Research Scholor Protein Dynamics lab Dept of Chemistry IIT Powai, Mumbai, 400076 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] mpi run
During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work. I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run. Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for your problems, just cause I once confused about why mine 4cpus barely used before too. Best, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carsten Kutzner [ckut...@gwdg.de] Sent: Thursday, July 08, 2010 4:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy minimisation of solvated protein - Tutorial
remember to change the pbc = xyz from pbc = no. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, June 22, 2010 12:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation of solvated protein - Tutorial Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher eltha...@ualberta.ca wrote: Hi, I have the same problem as listed below back in February. I am using the latest gromacs version (4.0.7) and tried the solution below by entering genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of making the output as pdb file. Yet the same result occurs with the same error message. One of the box lengths is smaller than twice the cut-off length. Please let me know what other options I can try. Thanks! nayef -- original message below -- Hi Anna, You should mention the version of Gromacs you're using. One of the versions did not write the box correctly to pdb files, which I think happened in your case. If you take as the solvation step genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of writing output to 1qlz-water.pdb, I think you should be fine. The reason for writing a .pdb file is the easier visualization with a multitude of programs. Thanks for your interest in the tutorial. Cheers, Tsjerk On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk wrote: Hi, I've been trying to go through the 'Introduction to Molecular Dynamics Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the tutorials listed on the GROMACS website. I've got to the stage where I am performing energy minimisation on my solvated protein but when I use grompp to create the .tpr file for mdrun, I get the error message: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I am using the protein with pdb ID 1QLZ, one of the suggested structures for the tutorial and have so far carried out the following commands: % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname NA+ -nname CL- % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr after which I receive the error message. The minim_pbd.mdp file I use in the last grompp command is the same as minim.mdp used in previous grompp commands (the latter file I downloaded as part of the tutorial) except that the line 'pbc = no' has been replaced by 'pbc = xyz'. I have tried increasing the value of 'd' in the editconf command, to 2,3 and even 8 but this doesn't make any difference. (I have read that it is not a good idea to tamper with the cut-off values so have avoided doing that) The box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... Anna -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
RE: [gmx-users] No default Proper Dih. types
Check your error message more, They will tell you which line in which .itp file there is No default Proper Dih. types. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Saturday, June 19, 2010 8:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] No default Proper Dih. types fancy2012 wrote: Dear GMX users, When I run grompp, I got this error No default Proper Dih. types, how should I figure it out? Thanks in advance! Whatever force field you're trying to use does not have a dihedral term for that type of dihedral. Either obtain suitable parameters from the literature, parameterize it yourself, or use a different force field that can accommodate this term. -Justin All the best, fancy -- 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the box lengths
Well... There is one line in try2-water.pdb, shows as below TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 86.185 86.185 86.185 60.00 60.00 90.00 P 1 1 Do you think something was wrong during genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ -nname CL- Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:41 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Well, there's ya problem :-) That specifies the box dimensions. Have a look at try2-water.pdb as well, then you should be able to pin down where the issue has arisen. Appears that one of those steps have failed to write the box dimensions. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 3:37 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths There is none CRYST1 line in the file try2-water-ions.pdb. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:24 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths What is the contents of the CRYST1 line in the file try2-water- ions.pdb? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the box lengths
Thanks all, I know what's wrong now. I forgot to set pbc = xyz earlier. By the way, is it normal for test failure of the gmxtest? such as :~/src/gmxtest$ ./gmxtest.pl complex FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 3 out of 14 complex tests FAILED Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Tuesday, June 15, 2010 1:56 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Well... There is one line in try2-water.pdb, shows as below TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 86.185 86.185 86.185 60.00 60.00 90.00 P 1 1 Do you think something was wrong during genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ -nname CL- Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:41 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Well, there's ya problem :-) That specifies the box dimensions. Have a look at try2-water.pdb as well, then you should be able to pin down where the issue has arisen. Appears that one of those steps have failed to write the box dimensions. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 3:37 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths There is none CRYST1 line in the file try2-water-ions.pdb. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:24 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths What is the contents of the CRYST1 line in the file try2-water- ions.pdb? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the box lengths
Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem. integrator = steep emtol = 1.0 nsteps = 500 nstenergy = 1 energygrps = System ns_type = simple coulombtype = cut-off rcoulomb= 1.0 rvdw= 1.0 constraints = none pbc = xyz Thanks for any advice, Best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the box lengths
___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem. Well, what are your box vectors? If they are 2 nm, you will get this error because of the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin system size : 4.581 2.380 2.715 (nm) diameter: 4.889 (nm) center : -0.012 0.003 -0.904 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 9.678 9.664 5.461 (nm) new center : 9.667 9.667 4.557 (nm) new box vectors : 12.889 12.889 12.889 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1514.05 (nm^3) This one I set was really large, but still showed that problems. Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the box lengths
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem. Well, what are your box vectors? If they are 2 nm, you will get this error because of the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin system size : 4.581 2.380 2.715 (nm) diameter: 4.889 (nm) center : -0.012 0.003 -0.904 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 9.678 9.664 5.461 (nm) new center : 9.667 9.667 4.557 (nm) new box vectors : 12.889 12.889 12.889 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1514.05 (nm^3) This one I set was really large, but still showed that problems. What problems? The same error about the box lengths being shorter than twice the cutoff? I don't think that's possible, given those vectors, if you're keeping your cutoffs at 1.0 nm. -Justin I do keep the cut-off. That's I do not know why. Four times had been tried. Thanks, lina -- 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the box lengths
I used the same commands trying another proteins, but no problems. So it's not the reason about the commands I used. It did not contain the same number of molecules after genion when I changed the box size. The pressure coupling was not on, and I did not reach this steps. The problem I had just the steps I did the energy minimization after ions (NA+ and CL-) added. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 6:48 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Please copy and paste in the commands you are using, and the output. I suspect you have made your box bigger, but it still contains the same number of molecules and you still have pressure coupling on. So when you start the simulation, not surprising that the box compresses again and goes under 2nm again. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 12:04 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem. Well, what are your box vectors? If they are 2 nm, you will get this error because of the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi on -Justin system size : 4.581 2.380 2.715 (nm) diameter: 4.889 (nm) center : -0.012 0.003 -0.904 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 9.678 9.664 5.461 (nm) new center : 9.667 9.667 4.557 (nm) new box vectors : 12.889 12.889 12.889 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1514.05 (nm^3) This one I set was really large, but still showed that problems. What problems? The same error about the box lengths being shorter than twice the cutoff? I don't think that's possible, given those vectors, if you're keeping your cutoffs at 1.0 nm. -Justin I do keep the cut-off. That's I do not know why. Four times had been tried. Thanks, lina -- 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use
RE: [gmx-users] the box lengths
cut-off of 1 nm Will try to add 43 NA+ ions and 41 CL- ions. /// After vim the topol.top and the minim.mdp which pbc=no to pbc=xyz, grompp -f minim.mdp -c try2-water-ions.pdb -p topol.top -o try2-EM-water-ions.tpr double-checking input for internal consistency... ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. /// but if I still used the pbc=no, it will work fine at this steps. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 11:15 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths As already mentioned by Justin, unless you copy and paste the commands and output you got, for us to see, we can only have stabs in the dark (which is what I did since you are missing lots of information on what you are actually doing) to what is actually going on. And don't type in the commands into your email client, physically go and copy and paste the text in, otherwise you are filtering it through your own mind. Go and run the series of commands that work, copy / paste the results for us to see. Then go and run the series of commands that don't work, copy / paste again. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 12:32 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths I used the same commands trying another proteins, but no problems. So it's not the reason about the commands I used. It did not contain the same number of molecules after genion when I changed the box size. The pressure coupling was not on, and I did not reach this steps. The problem I had just the steps I did the energy minimization after ions (NA+ and CL-) added. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 6:48 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Please copy and paste in the commands you are using, and the output. I suspect you have made your box bigger, but it still contains the same number of molecules and you still have pressure coupling on. So when you start the simulation, not surprising that the box compresses again and goes under 2nm again. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of #ZHAO LINA# Sent: Tuesday, 15 June 2010 12:04 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 10:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, June 14, 2010 9:33 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the box lengths #ZHAO LINA# wrote: Hi, First time I meet this problem, ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. I just followed the advice increase the box size, I tried twice in the editconf about the box size, actually this box is really large enough for the testing consideration, but still has the same problem
RE: [gmx-users] the box lengths
There is none CRYST1 line in the file try2-water-ions.pdb. Thanks and regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:24 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths What is the contents of the CRYST1 line in the file try2-water-ions.pdb? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] velocity autocorrelation function.
Hi, When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation functions). There is a very general (simple) descriptions. I feel I need a bit more deep-relevant references. gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function, it's really hard for me to read such a nice codes. If I want to know much more about the specific formula of velocity autocorrelation functions which is being used in gromacs and how it's implemented, which way I should go? Great appreciation for any advice, Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] velocity autocorrelation function.
On 2010-06-03 08.23, #ZHAO LINA# wrote: Hi, When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation functions). There is a very general (simple) descriptions. I feel I need a bit more deep-relevant references. gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function, it's really hard for me to read such a nice codes. If I want to know much more about the specific formula of velocity autocorrelation functions which is being used in gromacs and how it's implemented, which way I should go? Great appreciation for any advice, Best Regards, lina This is described quite well in the textbook by Allen adn Tildesley (1987) you will find the reference in the manual. Thanks, I am reading this ebook now. Just wonder there are some latest ones. Best Regards, lina -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xml
During configuration, there is something about xml. a functions in analysis --without-xml do not link to the xml2 library, disallows the use of certain file formats 1. which file formats did they specify to? 2. Can gromacs handle the PDBML file? Thanks and regards, lina winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: loab imbalance
lina wrote: On 6/04/2010 5:39 PM, lina wrote: Hi everyone, Here is the result of the mdrun which was performed on 16cpus. I am not clear about it, was it due to using MPI reason? or some other reasons. Writing final coordinates. Average load imbalance: 1500.0 % Part of the total run time spent waiting due to load imbalance: 187.5 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % NOTE: 187.5 % performance was lost due to load imbalance in the domain decomposition. You ran an inefficient but otherwise valid computation. Check out the manual section on domain decomposition to learn why it was inefficient, and whether you can do better. Mark I search the decomposition keyword on Gromacs manual, no match found. Are you positive about that? Thanks any way, but can you make it more The title of section 3.17 is Domain Decomposition and discusses the algorithm and mdrun parameters relevant to controlling performance. -Justin Sorry, the acroread is really not sensitive in searching domain or decomposition on version 3.3. I did the same search on version 3.2 and I found it. I am not so familiar with this manual. Thanks again. lina Since you performance roughly doubles when going from 8 to 16 cores, I think there is no significant load imbalance and there is a bug in the routine that calculates the total load imbalance. In my previous mail I asked which Gromacs version you are using. Could you please tell me this? Berk Hi, it's version 4.0.7. Sorry, mainly I will consider using the latest (better stable) version, so last time I forgot to answer you. I also run it on cluster before, it does not have such problems (by my careless mistakes, I overwrite it when I tried to compare the results from the multicores, and it's days ago and I barely could not remember exactly, I worried I might ignore the problems, so I re-run it again, and the results will wait for a while). Thanks for those suggestions they gave for me to read the manuals. The machine I used is single multicore machine with 64 bits kernel. Thanks and regards, lina winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hessian Matrix
Hi everyone, I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output. Below is the command I used in the scripts of my last two trial. 1) ## To run on 16 cpus #PBS -l nodes=2:ppn=8 ## program to run mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 2) ## program to run mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx Thanks and best, lina winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Hessian Matrix
Hi, I just simply did a change in .mdp file. Now the integrator = nm after grompp, 1) below is the error of mdrun -s em.tpr -mtx em.mtx Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 4118944041 elements of size 4 for full_matrix (called from file ../../../../src/mdlib/minimize.c, line 2219) 2) Seems the one run in cluster choked there like this in md.log. Linking all bonded interactions to atoms There are 2106 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.76 nm Y 1.07 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.000 nm two-body bonded interactions (-rdd) 1.000 nm multi-body bonded interactions (-rdd) 1.000 nm Thanks for further suggestion, lina #ZHAO LINA# wrote: Hi everyone, I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output. Below is the command I used in the scripts of my last two trial. 1) ## To run on 16 cpus #PBS -l nodes=2:ppn=8 ## program to run mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 2) ## program to run mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx Probably because the Hessian is only relevant when doing normal mode calculations (or perhaps L-BFGS minimization). I suspect that if you're not using the nm integrator, then you're not going to get the Hessian. -Justin Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi_run issue
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place wrong, seems no
files came out after several hours running
Is anyone please help me to modify it, and how can know the process of its
running in the cluster.
Thanks and best regards,
Elsa
#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
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[gmx-users] RE: gmx-users Digest, Vol 69, Issue 145
Hi,
Here is the example file I based on to modify,
mpi.sh
#!/bin/bash
#
## Specify the job name
#PBS -N jobname
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE ./myprog
My working directory is ${HOME}/Jobs/1A7W/tryScript. By the way, I do not know
the NODEFILE mean.
Thanks and best regards,
Elsa
--
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place
wrong, seems no files came out after several hours running
Is anyone please help me to modify it, and how can know the
process of its running in the cluster.
We can't know the best procedure for your cluster because we haven't read its
documentation or talked to its admins... (hint, hint)
Thanks and best regards,
Elsa
#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1
This looks wrong. PBS usually has flags that let you specify running the job in
directory from which submission occured - use them.
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
If PBS is defining $PBS_NODEFILE to point to some file it creates, then that
file won't be local to the directory you've arbitrarily changed to, so NCPUS
won't get defined suitably, so mpirun won't work.
I'd suggest you start again from some example script that is known to work on
your cluster and modify only the mpirun line.
Mark
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
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Message: 2
Date: Thu, 28 Jan 2010 16:03:50 +0100
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4b61a756.7060...@xray.bmc.uu.se
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
afsaneh maleki skrev:
thanks dear justin'
it is right that the output of the analysis tools generally writes
axis labels and data set legends. in hblife.xyg file is written that
x axis label Time (ps) and the last time is written 14300.001
whereas my simulated time is 4 ps not 143000.00 ps
i send you this file
I don't remember the details about the calculation of lifetimes, but I
believe it's an estimate of how the half lifes of hydrogen bonds. You
can also get this quantity, along with the kinetic constants and
energies for hb breaking and frormation, using -ac. If I remember
correctly, -ac uses a more reliable method.
Erik
Best wishes,
Afsaneh
On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
afsaneh maleki wrote:
Hi,
would you please elaborate the first column in the hblife.xvg
file?
hblife.xyg is the output of the following command:
g_hbond -life hblife.xvg
this column don't show the real time in simulated system.what
are these times?
Check the headers in the .xvg file; the output of the analysis
tools generally writes axis labels and data set legends. If it
still doesn't make sense, post a snippet of your file.
-Justin
thanks in advance,
Afsaneh
--
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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[gmx-users] Re:mpi_run issue
Hi everyone,
I still do not know how to modify it.
Thanks,
Elsa
--
Hi,
Here is the example file I based on to modify,
mpi.sh
#!/bin/bash
#
## Specify the job name
#PBS -N jobname
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE ./myprog
My working directory is ${HOME}/Jobs/1A7W/tryScript. By the way, I do not know
the NODEFILE mean.
Thanks and best regards,
Elsa
--
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place
wrong, seems no files came out after several hours running
Is anyone please help me to modify it, and how can know the
process of its running in the cluster.
We can't know the best procedure for your cluster because we haven't read its
documentation or talked to its admins... (hint, hint)
Thanks and best regards,
Elsa
#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1
This looks wrong. PBS usually has flags that let you specify running the job in
directory from which submission occured - use them.
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
If PBS is defining $PBS_NODEFILE to point to some file it creates, then that
file won't be local to the directory you've arbitrarily changed to, so NCPUS
won't get defined suitably, so mpirun won't work.
I'd suggest you start again from some example script that is known to work on
your cluster and modify only the mpirun line.
Mark
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
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Message: 2
Date: Thu, 28 Jan 2010 16:03:50 +0100
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4b61a756.7060...@xray.bmc.uu.se
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
afsaneh maleki skrev:
thanks dear justin'
it is right that the output of the analysis tools generally writes
axis labels and data set legends. in hblife.xyg file is written that
x axis label Time (ps) and the last time is written 14300.001
whereas my simulated time is 4 ps not 143000.00 ps
i send you this file
I don't remember the details about the calculation of lifetimes, but I
believe it's an estimate of how the half lifes of hydrogen bonds. You
can also get this quantity, along with the kinetic constants and
energies for hb breaking and frormation, using -ac. If I remember
correctly, -ac uses a more reliable method.
Erik
Best wishes,
Afsaneh
On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
afsaneh maleki wrote:
Hi,
would you please elaborate the first column in the hblife.xvg
file?
hblife.xyg is the output of the following command:
g_hbond -life hblife.xvg
this column don't show the real time in simulated system.what
are these times?
Check the headers in the .xvg file; the output of the analysis
tools generally writes axis labels and data set legends. If it
still doesn't make sense, post a snippet of your file.
-Justin
thanks in advance,
Afsaneh
--
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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