[gmx-users] Charge assignment
Hi everyone. I'm working on getting parameters for a protein system that has some linker residues in it. These linkers are nothing too strange, they just have some amine groups. I can get bonded parameters from the prodrg server. I know the charge groups are unreliable. I'm using the 53A6 parameter set, and I read how the charges there were derived. They specifically did the iteration of parameters manually to give the same charges for the same functional groups. Does this mean I can take charges from the same functional groups in the rtp files for amino acids and use those charges in my linkers? If it is necessary to validate, should that be done on the linkers as molecules in their acidic, unlinked form? Thanks everyone. -- 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] asking help for simulation of protein in 8M urea
Dear all, I want to a protein simulation in 8M urea. Can anyone suggest me any introductory tutorial on that. Thank you 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/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] Re: [gmx-user]Error by pdb2gmx (Mark Abraham)
Hi, Please leave some context in your email replies. Whoever replied last time has their own work and probably responded to other people's problems on here... They won't remember your context as well as you do :-). IIRC, I pointed out the problem was probably in what you'd done with the .rtp file. Your DRG content looks OK at a glance, but if you've dumped in that file with (say) inappropriate line-endings, then that could be your problem. Mark - Original Message - From: 佘安奇 she_an...@yahoo.cn Date: Thursday, May 20, 2010 11:32 Subject: [gmx-users] Re: [gmx-user]Error by pdb2gmx (Mark Abraham) To: gmx-users@gromacs.org --- | Dear Mark: I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. And the rtp of my molecule is in the attached file DRG.txt. Thank you very much! Angel | --- -- 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] asking help for simulation of protein in 8M urea
On 05/20/2010 09:05 AM, caty hacker wrote: Dear all, I want to a protein simulation in 8M urea. Can anyone suggest me any introductory tutorial on that. Thank you in advance. I think a tutorial is useless for such a simulation. Papers are the best reference depending on what you want to simulate and on what you want to see: if you are trying to simulate the unfolding there are several publications that discuss the major issues of the field, i.e. a. which ff and/or urea topology to use b. which computational technique (REMD, MD, MetaMD ...) to use So ... what's your goal ? :) At the moment I am too working on some systems that require the usage of urea and doing a bit of set up for AMBER FF, whereas in the past I have used a topology for the last GROMOS FF. Cheers Luca -- -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 38027 France E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com) Telephone: +33.438783889 -- Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses. Jake: Hit it. (The Blues Brothers) -- 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] adding constraints
Hi all, I want to add constraints for bond length of a ligand.Where do I place the constraints statement in the .rtp file or in the .top file? Subarna Thakur -- 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] g_helixorient issue
Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0. --- # # g_helixorient is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Cumulative local helix tilt @xaxis label Time(ps) @yaxis label Tilt (degrees) @TYPE xy 2 03.595408201224.23953723907 5.74576044083 5.64022207262.993204355243.96751046181 6.915472984316.317507743845.708302021031.80687570572 7.904520511635.554297924044.3107757568413.4955091476 10.86933803566.696783542631.318642735488.81209087372 15.092011451716.443498611513.575768470812.6605091095 9.89414119725.959523200992.222523212434.23878717422 11.912554740915.239257812510.13733291632.50473761559 2.987089633940 4 0 0.1932501047851.85375285149 4.660104274755.734657764433.596650362013.71966171265 5.862170696265.205702304844.286367416385.67181348801 11.8561506271 10.8149480825.253306865693.01665711403 3.188149690636.1265802383410.878685951213.1984567642 15.8662624359 17.9544162759.977549552923.82837629318 7.255657672884.875072002413.158228397375.81644439697 6.565203189857.591495513925.399117946622.35803961754 4.941868305210 6.0047684 02.78084087372 2.5538725853 3.536648511898.4336194992114.915288925213.8589410782 6.6992340087911.7872600555 17.235452652 10.804684639 12.89069366468.979190826425.7719144821210.7680120468 9.713017463688.8874626159711.251163482710.2795152664 8.691395759587.554894447333.242376565931.74266982079 2.973826408394.069952487953.690156698232.21045541763 2.921667337424.463324546814.281089782713.39760541916 4.103402614590 8 0 5.4110045433 5.6742272377 8.93139266968 11.787487038.761271476755.92636489868 2.527382135396.2623438835110.01829242712.88692927361 8.243747711184.966527462018.7450408935517.1016178131 14.6491327286 8.43484878549.4807758331311.1341199875 11.373338699314.302871704112.88017845157.42469358444 3.84174942974.058297157291.937186241152.07590007782 6.721652030949.818412780769.60572147369 6.2793135643 4.37946939468 --- How to visualize this file properly? Why is the .xvg file written in this manner? Any suggestion is welcome. Regards, Anirban -- 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] asking help for simulation of protein in 8M urea
Hi Caty, In addition to Luca's comments, also consider what you mean with 8M. Molarity is defined as mole per liter, but the addition of urea may have an effect on the volume, such that adding a volume x urea to a volume y water does not yield a volume x+y. Especially with such high concentrations you might be better off with molalities (mole/kg). Then you probably want to first generate a box of urea in water by adding a adding a box of water to a box of urea and letting it diffuse (at a high temperature). But only after you figured out the answers to Luca's questions :) Cheers, Tsjerk On Thu, May 20, 2010 at 9:32 AM, Luca Mollica luca.moll...@ibs.fr wrote: On 05/20/2010 09:05 AM, caty hacker wrote: Dear all, I want to a protein simulation in 8M urea. Can anyone suggest me any introductory tutorial on that. Thank you in advance. I think a tutorial is useless for such a simulation. Papers are the best reference depending on what you want to simulate and on what you want to see: if you are trying to simulate the unfolding there are several publications that discuss the major issues of the field, i.e. a. which ff and/or urea topology to use b. which computational technique (REMD, MD, MetaMD ...) to use So ... what's your goal ? :) At the moment I am too working on some systems that require the usage of urea and doing a bit of set up for AMBER FF, whereas in the past I have used a topology for the last GROMOS FF. Cheers Luca -- -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 38027 France E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com) Telephone: +33.438783889 -- Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses. Jake: Hit it. (The Blues Brothers) -- gmx-users mailing list gmx-us...@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 -- 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 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] DSSP
Hi Shahid, I have fixed the problem in do_dssp. You can either pull the newest release-4-0-patches branch from the git repository or change ./src/tools/do_dssp.c, line 80 from snew(ssbuf,nres+10); to: snew(ssbuf, 2*nres-1); Carsten On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote: Hi, there was a problem in do_dssp when used on proteins with more than 10 chains. Is this the case? I just saw that I only fixed that in the head, but not in 4.0.x. Carsten On May 18, 2010, at 3:49 PM, shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
[gmx-users] g_helixorient issue
Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0. --- # # g_helixorient is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Cumulative local helix tilt @xaxis label Time(ps) @yaxis label Tilt (degrees) @TYPE xy 2 03.595408201224.23953723907 5.74576044083 5.64022207262.993204355243.96751046181 6.915472984316.317507743845.708302021031.80687570572 7.904520511635.554297924044.3107757568413.4955091476 10.86933803566.696783542631.318642735488.81209087372 15.092011451716.443498611513.575768470812.6605091095 9.89414119725.959523200992.222523212434.23878717422 11.912554740915.239257812510.13733291632.50473761559 2.987089633940 4 0 0.1932501047851.85375285149 4.660104274755.734657764433.596650362013.71966171265 5.862170696265.205702304844.286367416385.67181348801 11.8561506271 10.8149480825.253306865693.01665711403 3.188149690636.1265802383410.878685951213.1984567642 15.8662624359 17.9544162759.977549552923.82837629318 7.255657672884.875072002413.158228397375.81644439697 6.565203189857.591495513925.399117946622.35803961754 4.941868305210 6.0047684 02.78084087372 2.5538725853 3.536648511898.4336194992114.915288925213.8589410782 6.6992340087911.7872600555 17.235452652 10.804684639 12.89069366468.979190826425.7719144821210.7680120468 9.713017463688.8874626159711.251163482710.2795152664 8.691395759587.554894447333.242376565931.74266982079 2.973826408394.069952487953.690156698232.21045541763 2.921667337424.463324546814.281089782713.39760541916 4.103402614590 8 0 5.4110045433 5.6742272377 8.93139266968 11.787487038.761271476755.92636489868 2.527382135396.2623438835110.01829242712.88692927361 8.243747711184.966527462018.7450408935517.1016178131 14.6491327286 8.43484878549.4807758331311.1341199875 11.373338699314.302871704112.88017845157.42469358444 3.84174942974.058297157291.937186241152.07590007782 6.721652030949.818412780769.60572147369 6.2793135643 4.37946939468 --- How to visualize this file properly? Why is the .xvg file written in this manner? Any suggestion is welcome. Regards, Anirban -- 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] Essential Dynamics
Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. Thanks 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] Essential Dynamics
On 05/20/2010 10:40 AM, Carla Jamous wrote: Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. Thanks Carla http://www.ncbi.nlm.nih.gov/pubmed/8108382 AKA how the molecular dynamics simulations were decomposed into essential motions for the first time. I don't know if it's suitable for beginners or not: for sure it represents the begin of the story ... :) Luca -- -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 38027 France E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com) Telephone: +33.438783889 -- Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses. Jake: Hit it. (The Blues Brothers) -- 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] Essential Dynamics
On 05/20/2010 10:40 AM, Carla Jamous wrote: Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. Thanks Carla and of course, in a more practical way: http://www.gromacs.org/Documentation/How-tos/Essential_Dynamics L -- -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 38027 France E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com) Telephone: +33.438783889 -- Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses. Jake: Hit it. (The Blues Brothers) -- 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] Re: acetonitrile from amber to gromacs
Alan schrieb: Dear Vedat, On Wed, May 19, 2010 at 20:36, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: @rui acpypi -i ch3cn_210.pdb says: cannot find template for residue C3N in our library. and indeed, there's no residue C3N in my ffamber99sb.rtp file (and i don't know, how to use it in order to generate my topology or even an rtp file?!) Have a bit of patience and try to read a bit more about ACPYPE. 1) Read the info there, I am sure you'll find it useful; 2) You'll learn that you need to have just one molecule in a pdb and not the whole box if you want the topologi of C3N. 3) It took me 2s to get the topology with acpype but months to write the code, so if you'd take some few minutes to read and use an updated version (it's not acpypi anymore BTW)... thanks for your helpful hints. i updated acpype, created a pdb file with a single molecule and ran acpype -i ch3cn_210_single.pdb which generated an .itp and other interesting files. that's nice. (remember, i want to use gromacs with amber99sb force field and i downloaded 3 files from the amber site: ch3cn_210.pdb, frcmod.ch3cn,prep.ch3cn.have you ever seen their content?) 1) the charges do not match the ones listed in the prep.ch3cn file. shall i just change them by hand accordingly? 2) dummy atoms as listed in the prep.ch3cn are not present in the new .itp file. 3) the force constants seem totally different. shall i again just adjust them to the original file obtained from the amber site? is there another way of using acpype, with a proper args list, that i should use in this situation? i know, that's many questions, but is has to be done! BTW, how did you get this message cannot find template for residue C3N in our library? i got that message *within* the following output when running: acpype -i ch3cn_210.pdb [...] Warning: cannot find template for residue C3N in our library. You will not be able to save prmtop for this molecule. Warning: cannot find template for residue C3N in our library. You will not be able to save prmtop for this molecule. [gtkleap]$ #check C3N [gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd Error: dparm pchg does not exist! ++end_quote+ ERROR: Sleap failed == Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd' Total time of execution: 7s acpype.googlecode.com http://acpype.googlecode.com Regards, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- 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: energy decreasing in NVE simulation
Dear Erik, Thank you so much for your prompt reply. I appreciate it. Yun-an Yan Erik Marklund writes: For more exotic NVE-systems I had to do some or several of the following things to get stable Etot: * have an even shorter timestep than one would expect from the applied constraints and such. I will try a timestep with 0.5 fs. * use double precision. The double precision is already in use. * apply the constraints with lower tolerance/more iterations etc. I thought shake_tol = 1.e-8 is small enough. May I try an even smaller value? Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is recommended instead of shake? Then there's a few things I notice in your setup: * I see that you do not use constrints at all. I would give it a shot. I will try. * Why do you have two separate comm-grps? Since it is a solute-solvent fashion MD, I am trying to keeping the solute part close the center of the simulation box. But it does not work in this way. Do you have any idea about that? Erik Marklund -- --- 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 erikm at 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
Re: [gmx-users] Re: Re: energy decreasing in NVE simulation
Hi Yun-an Yan, In addition to the other things, COMM removal is also a source of energy drift. It is better to center your solute afterwards. Cheers, Tsjerk On Thu, May 20, 2010 at 1:05 PM, Yan Yun-an yun-an@uni-rostock.de wrote: Dear Erik, Thank you so much for your prompt reply. I appreciate it. Yun-an Yan Erik Marklund writes: For more exotic NVE-systems I had to do some or several of the following things to get stable Etot: * have an even shorter timestep than one would expect from the applied constraints and such. I will try a timestep with 0.5 fs. * use double precision. The double precision is already in use. * apply the constraints with lower tolerance/more iterations etc. I thought shake_tol = 1.e-8 is small enough. May I try an even smaller value? Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is recommended instead of shake? Then there's a few things I notice in your setup: * I see that you do not use constrints at all. I would give it a shot. I will try. * Why do you have two separate comm-grps? Since it is a solute-solvent fashion MD, I am trying to keeping the solute part close the center of the simulation box. But it does not work in this way. Do you have any idea about that? Erik Marklund -- --- 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 erikm at xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing list gmx-us...@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 -- 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 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] g_helixorient issue
Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0. --- # # g_helixorient is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Cumulative local helix tilt @xaxis label Time(ps) @yaxis label Tilt (degrees) @TYPE xy 2 03.595408201224.23953723907 5.74576044083 5.64022207262.993204355243.96751046181 6.915472984316.317507743845.708302021031.80687570572 7.904520511635.554297924044.3107757568413.4955091476 10.86933803566.696783542631.318642735488.81209087372 15.092011451716.443498611513.575768470812.6605091095 9.89414119725.959523200992.222523212434.23878717422 11.912554740915.239257812510.13733291632.50473761559 2.987089633940 4 0 0.1932501047851.85375285149 4.660104274755.734657764433.596650362013.71966171265 5.862170696265.205702304844.286367416385.67181348801 11.8561506271 10.8149480825.253306865693.01665711403 3.188149690636.1265802383410.878685951213.1984567642 15.8662624359 17.9544162759.977549552923.82837629318 7.255657672884.875072002413.158228397375.81644439697 6.565203189857.591495513925.399117946622.35803961754 4.941868305210 6.0047684 02.78084087372 2.5538725853 3.536648511898.4336194992114.915288925213.8589410782 6.6992340087911.7872600555 17.235452652 10.804684639 12.89069366468.979190826425.7719144821210.7680120468 9.713017463688.8874626159711.251163482710.2795152664 8.691395759587.554894447333.242376565931.74266982079 2.973826408394.069952487953.690156698232.21045541763 2.921667337424.463324546814.281089782713.39760541916 4.103402614590 8 0 5.4110045433 5.6742272377 8.93139266968 11.787487038.761271476755.92636489868 2.527382135396.2623438835110.01829242712.88692927361 8.243747711184.966527462018.7450408935517.1016178131 14.6491327286 8.43484878549.4807758331311.1341199875 11.373338699314.302871704112.88017845157.42469358444 3.84174942974.058297157291.937186241152.07590007782 6.721652030949.818412780769.60572147369 6.2793135643 4.37946939468 --- How to visualize this file properly? Why is the .xvg file written in this manner? Any suggestion is welcome. Regards, Anirban -- 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] breaking down total energy
Moeed wrote: Hello Justin, Thanks for your comments. Actually, since I am interested in only interaction energies *between* molecules I thought by excluding energies between atoms on a single chain what I get from nonbonded interactions would not include 1-4 interactions. OK, I see what you're doing, your approach was just wrong. The simplest thing to do is the following. First, run a normal MD simulation, no fancy exclusions or anything, until you have produced a stable hexane system that reproduces whatever observable quantities you have decided upon. Know what you're looking for first! Then, modify the topology to add the exclusions you want. It is a whole lot easier to simply increase the number given in nrexcl within the [moleculetype] definition to take care of all possible interactions than anything else. There's nothing wrong with doing it manually (somewhere *after* the atoms have been defined, but before the end of the [moleculetype] definition), it's just more work. There is no need for special energygrps or energygrp_excl for your purpose, since those exclusions are applied to intermolecular interactions, not intramolecular interactions, and they are not dependent upon [exclusions] defined in the topology. Once you have a suitably modified topology, use mdrun -rerun on the original trajectory. -Justin * This is from previous posts: Question: Can I not take for instance LJ energy values which are coming from a specific NO. of molecuels in simulation box and calculate interaction energies for pairs or mol number of molecules? Your answer: Not easily. You will still have intramolecular terms that are not covered by the 1-4 interactions. *For example, if the two ends of your molecule interact with one another, this interaction will contribute to your nonbonded energies.* * That is why I thought I have to exclude interaction in a single chain between atoms, so that for instance atoms 1 and 20 do not see each other. I manual I found only about how extra exlusion within a molecue cab added in [exclusions].. I dont think this helps me. How can I define all possible intramolecular exclusions in order to save only intermolecular energy contributions? top file: Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Hexane 3 [ exclusions ] ?? [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_157 1HEX C1 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1HEXH11 1 0.06 1.008 ; qtot -0.12 3 opls_140 1HEXH12 1 0.06 1.008 ; qtot -0.06 4 opls_140 1HEXH13 1 0.06 1.008 ; qtot 0 5 opls_158 1HEX C2 2 -0.12 12.011 ; qtot -0.12 6 opls_140 1HEXH21 2 0.06 1.008 ; qtot -0.06 7 opls_140 1HEXH22 2 0.06 1.008 ; qtot 0 8 opls_158 1HEX C3 3 -0.12 12.011 ; qtot -0.12 9 opls_140 1HEXH31 3 0.06 1.008 ; qtot -0.06 10 opls_140 1HEXH32 3 0.06 1.008 ; qtot 0 11 opls_158 1HEX C4 4 -0.12 12.011 ; qtot -0.12 12 opls_140 1HEXH41 4 0.06 1.008 ; qtot -0.06 13 opls_140 1HEXH42 4 0.06 1.008 ; qtot 0 14 opls_158 1HEX C5 5 -0.12 12.011 ; qtot -0.12 15 opls_140 1HEXH51 5 0.06 1.008 ; qtot -0.06 16 opls_140 1HEXH52 5 0.06 1.008 ; qtot 0 17 opls_157 1HEX C6 6 -0.18 12.011 ; qtot -0.18 18 opls_140 1HEXH61 6 0.06 1.008 ; qtot -0.12 19 opls_140 1HEXH62 6 0.06 1.008 ; qtot -0.06 20 opls_140 1HEXH63 6 0.06 1.008 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 8 1 8 9 1 810 1 811 1 1112 1 1113 1 1114 1 1415 1 1416 1 1417 1 1718 1 1719 1 1720 1 [ pairs ] ; aiaj functc0c1c2c3 1 9 1 110 1 111 1 2 6 1 2 7 1 2 8 1 3 6 1 3 7 1 3 8 1
Re: [gmx-users] Charge assignment
Michael McGovern wrote: Hi everyone. I'm working on getting parameters for a protein system that has some linker residues in it. These linkers are nothing too strange, they just have some amine groups. I can get bonded parameters from the prodrg server. I know the charge groups are unreliable. I'm using the 53A6 parameter set, and I read how the charges there were derived. They specifically did the iteration of parameters manually to give the same charges for the same functional groups. Does this mean I can take charges from the same functional groups in the rtp files for amino acids and use those charges in my linkers? If it is necessary to validate, should that be done on the linkers as molecules in their acidic, unlinked form? Thanks everyone. Generally, the functional groups in the GROMOS parameter sets are very transferrable, as their derivation scheme would suggest. I suppose about the only validation you could do would be to prove that the properties of your linker molecules (whatever they may be) are reproduced by the application of these parameters when not joined to your protein. Reproduction of condensed-phase behavior and thermodynamic properties was the goal of the GROMOS derivation. -Justin -- 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
Re: [gmx-users] adding constraints
subarna thakur wrote: Hi all, I want to add constraints for bond length of a ligand.Where do I place the constraints statement in the .rtp file or in the .top file? Are you looking to constrain only one single bond length? If so, just add a [constraints] section to your topology. The .rtp file won't do you any good, unless you're looking to build a complete .rtp entry and re-process with pdb2gmx, but I don't know if [constraints] is a valid entry in an .rtp file. If you're looking to constrain all bond lengths, leave the topology alone and add constraints = all-bonds in your .mdp file. -Justin Subarna Thakur -- 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
Re: [gmx-users] enegry minimisation
Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title = protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 pbc = xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. I also want to ask what is the meaning of fx fy and fz : ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 1 1000 1000 1000 23 1 1000 1000 1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? Thanks in advance. -- Sonali Dhindwal --- On Wed, 19/5/10, Gaurav Goel gauravgoel...@gmail.com wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: sonali dhindwal sonali11dhind...@yahoo.co.in Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ... _ 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual. 2. Add define = -Dname to your mdp file 3. Add following lines to your topology file ; Include Position restraint file #ifdef name #include name.itp #endif 4. compile and run. I'm sure you will find mroe information on position-restrain simulation on gmx-users archive. -Gaurav On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Hello Gaurav, Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then do EM and then how to run a short MD simulation by constraining the protein backbone. Sorry to bother you, but as I am new to Gromacs, your help will be highly appreciable. Thanks in advance -- Sonali Dhindwal --- On Wed, 19/5/10, Gaurav Goel gauravgoel...@gmail.com wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 19 May, 2010, 6:44 PM After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion of protein structure. 4. Now run a MD on full system. for details looks here: http://www.google.com/url?sa=tsource=webct=rescd=2ved=0CBcQFjABurl=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdfei=jOPzS8a3Lab2MdX1_aAOusg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymgsig2=bY3NqXHmruR7eSLVyAuCHQ -Gaurav On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title= drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist= 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol
[gmx-users] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- 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] Re: OPLS-AA/L force field
The force fields have to be compatible but this way works fine. On 19 May 2010 12:50, Justin A. Lemkul jalem...@vt.edu wrote: Oliver Grant wrote: Can you not run pdb2gmx for each of your molecules that you want separate force fields for? Then cat the gro files, renumber and include the molecule types as .itp files in the .top file as below. If I'm doing anything wrong please let me know! :) Combining different force fields into a single system completely invalidates it, so yes, I'd say you're doing something wrong :) -Justin ; ;This is your topology file ;What If None Of Your Dreams Come True ? (E. Costello) ; ; Include forcefield parameters #include ffamber99sb.itp [ atomtypes ] from the top file of the non amber force field ;name bond_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom the top file of the amber force field, contains everything usually specified here under [molecule types]. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif #ifdef POSRES_CA #include CA_posre.itp #endif #include trisacc.itpfrom the top file of the non amber force field, contains charges etc. ; Include Position restraint file #ifdef POSRES_trisacc #include trisacc_posre.itp #endif ; Include water topology #include ffamber_tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 trisacc1 SOL 10697 Na 4 2010/5/19 you zou zou@live.com mailto:zou@live.com Hi Justin, Thank you for your help, But when I run x2top command there is one error that is: Can not find forcefield for atom C1-1 with 2 bonds Can not find forcefield for atom C4-4 with 2 bonds ... Program x2top, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a forcefield type for 6 out of 24 atoms I don't know how can I adjust this error. I have one more question again, this command give me a top file, if I want gro file of this pdb (drug that has removed from drug-enzyme complex) how can I do that? you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not? No. You can't use two different force fields in one simulation system. If I can't use this server, how can I make .gro file and .itp file for drug that remove from initial .pdb file? There are several programs in the User Contributions from the website, x2top (which is distributed with Gromacs), or you can build the topology by hand. No matter what you choose, you need a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. Thanks Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- gmx-users mailing listgmx-users@gromacs.org mailto: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
Re: [gmx-users] enegry minimisation
sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title= protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist= 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol= 1000.0 emstep = 0.01 pbc= xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. Well, you haven't properly defined position restraints. The default (produced by pdb2gmx) requires define = -DPOSRES not -DPOSRE. If you have for some reason modified the topology, then maybe your approach is correct, but otherwise your position restraints are not being applied. I also find it very curious that such substantial changes are taking place during a simple energy minimization. Are you sure the effects you are seeing are not simply due to the visualization software you are using guessing the incorrect secondary structure type? I have had that experience numerous times, especially in the case of beta-strands. DSSP tells me that, geometrically, I have beta-strands, but the visualization software renders coil structures. In any case, large structural deviations during EM suggest something fundamentally wrong with the model. Usually the changes in EM are small, since it is performed at 0 K. Only huge forces would cause any sort of structural change. I also want to ask what is the meaning of fx fy and fz : Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 1 1000 1000 1000 23 1 1000 1000 1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? These default values are typically quite sufficient to restrain the structure. -Justin Thanks in advance. -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: sonali dhindwal sonali11dhind...@yahoo.co.in Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ... _ 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual. 2. Add define = -Dname to your mdp file 3. Add following lines to your topology file ; Include Position restraint file #ifdef name #include name.itp #endif 4. compile and run. I'm sure you will find mroe information on position-restrain simulation on gmx-users archive. -Gaurav On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal sonali11dhind...@yahoo.co.in /mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Hello Gaurav, Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then do EM and then how to run a short MD simulation by constraining the protein backbone. Sorry to bother you, but as I am new to Gromacs, your help will be highly appreciable. Thanks in advance -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org
Re: [gmx-users] Re: OPLS-AA/L force field
Oliver Grant wrote: The force fields have to be compatible but this way works fine. I guess that depends on what you mean by works fine. If you mean that you can produce a stable simulation, then yes, it may work, but I would question the underlying premise of combining different force fields. If, for example, you're using an AMBER force field for, say, a protein, and OPLS for a small molecule, then what you're doing is wrong. The combination rules required by both force fields are different, as are the underlying derivation schemes and quite possibly some more details I'm not thinking about at the moment. I guess it all depends on what you mean (below) by non amber force field and how different it is from the actual requirements of the AMBER force field you're using. If this non amber force field was designed to be compatible with your chosen force field, and there was some suitable derivation scheme involved, then things will probably work. If you're mixing and matching parameter sets, be prepared for very tough questions from any reviewers who see your work. -Justin On 19 May 2010 12:50, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Oliver Grant wrote: Can you not run pdb2gmx for each of your molecules that you want separate force fields for? Then cat the gro files, renumber and include the molecule types as .itp files in the .top file as below. If I'm doing anything wrong please let me know! :) Combining different force fields into a single system completely invalidates it, so yes, I'd say you're doing something wrong :) -Justin ; ;This is your topology file ;What If None Of Your Dreams Come True ? (E. Costello) ; ; Include forcefield parameters #include ffamber99sb.itp [ atomtypes ] from the top file of the non amber force field ;name bond_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom the top file of the amber force field, contains everything usually specified here under [molecule types]. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif #ifdef POSRES_CA #include CA_posre.itp #endif #include trisacc.itpfrom the top file of the non amber force field, contains charges etc. ; Include Position restraint file #ifdef POSRES_trisacc #include trisacc_posre.itp #endif ; Include water topology #include ffamber_tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 trisacc1 SOL 10697 Na 4 2010/5/19 you zou zou@live.com mailto:zou@live.com mailto:zou@live.com mailto:zou@live.com Hi Justin, Thank you for your help, But when I run x2top command there is one error that is: Can not find forcefield for atom C1-1 with 2 bonds Can not find forcefield for atom C4-4 with 2 bonds ... Program x2top, VERSION 4.0.5 Source code
Re: [gmx-users] enegry minimisation
Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul jalem...@vt.edu wrote: sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title = protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 pbc = xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. Well, you haven't properly defined position restraints. The default (produced by pdb2gmx) requires define = -DPOSRES not -DPOSRE. If you have for some reason modified the topology, then maybe your approach is correct, but otherwise your position restraints are not being applied. I also find it very curious that such substantial changes are taking place during a simple energy minimization. Are you sure the effects you are seeing are not simply due to the visualization software you are using guessing the incorrect secondary structure type? I have had that experience numerous times, especially in the case of beta-strands. DSSP tells me that, geometrically, I have beta-strands, but the visualization software renders coil structures. In any case, large structural deviations during EM suggest something fundamentally wrong with the model. Usually the changes in EM are small, since it is performed at 0 K. Only huge forces would cause any sort of structural change. I also want to ask what is the meaning of fx fy and fz : Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 1 1000 1000 1000 23 1 1000 1000 1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? These default values are typically quite sufficient to restrain the structure. -Justin Thanks in advance. -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: sonali dhindwal sonali11dhind...@yahoo.co.in Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ... _ 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual. 2. Add define = -Dname to your mdp file 3. Add following lines to your topology file ; Include Position restraint file #ifdef name #include name.itp #endif 4. compile and run. I'm sure you will find mroe information on position-restrain simulation on gmx-users archive. -Gaurav On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal sonali11dhind...@yahoo.co.in /mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Hello Gaurav, Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then do EM and then how to run a short MD simulation by constraining the protein backbone. Sorry to bother you, but as I am new to Gromacs, your help will be highly appreciable. Thanks in advance -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com/* wrote: From: Gaurav Goel
Re: [gmx-users] Re: OPLS-AA/L force field
*I guess that depends on what you mean by works fine. * I mean the method of using pdb2gmx to generate a top and gro and then appending the gro files and including the .itp files in the .top file, works if you want to use two force fields. Originally I thought that was the question. *I guess it all depends on what you mean (below) by non amber force field* I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies for the confusion! Oliver -Justin On 20 May 2010 13:00, Justin A. Lemkul jalem...@vt.edu wrote: Oliver Grant wrote: The force fields have to be compatible but this way works fine. I guess that depends on what you mean by works fine. If you mean that you can produce a stable simulation, then yes, it may work, but I would question the underlying premise of combining different force fields. If, for example, you're using an AMBER force field for, say, a protein, and OPLS for a small molecule, then what you're doing is wrong. The combination rules required by both force fields are different, as are the underlying derivation schemes and quite possibly some more details I'm not thinking about at the moment. I guess it all depends on what you mean (below) by non amber force field and how different it is from the actual requirements of the AMBER force field you're using. If this non amber force field was designed to be compatible with your chosen force field, and there was some suitable derivation scheme involved, then things will probably work. If you're mixing and matching parameter sets, be prepared for very tough questions from any reviewers who see your work. -Justin On 19 May 2010 12:50, Justin A. Lemkul jalem...@vt.edu mailto: jalem...@vt.edu wrote: Oliver Grant wrote: Can you not run pdb2gmx for each of your molecules that you want separate force fields for? Then cat the gro files, renumber and include the molecule types as .itp files in the .top file as below. If I'm doing anything wrong please let me know! :) Combining different force fields into a single system completely invalidates it, so yes, I'd say you're doing something wrong :) -Justin ; ;This is your topology file ;What If None Of Your Dreams Come True ? (E. Costello) ; ; Include forcefield parameters #include ffamber99sb.itp [ atomtypes ] from the top file of the non amber force field ;name bond_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom the top file of the amber force field, contains everything usually specified here under [molecule types]. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif #ifdef POSRES_CA #include CA_posre.itp #endif #include trisacc.itpfrom the top file of the non amber force field, contains charges etc. ; Include Position restraint file #ifdef POSRES_trisacc #include trisacc_posre.itp #endif ; Include water topology #include ffamber_tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name
[gmx-users] Re: acetonitrile from amber to gromacs
Nice, glad you did progress. See below. On Thu, May 20, 2010 at 12:38, gmx-users-requ...@gromacs.org wrote: thanks for your helpful hints. i updated acpype, created a pdb file with a single molecule and ran acpype -i ch3cn_210_single.pdb which generated an .itp and other interesting files. that's nice. (remember, i want to use gromacs with amber99sb force field and i downloaded 3 files from the amber site: ch3cn_210.pdb, frcmod.ch3cn,prep.ch3cn.have you ever seen their content?) 1) the charges do not match the ones listed in the prep.ch3cn file. shall i just change them by hand accordingly? It doesn't match because it's using am1bcc, which was parametrised to reproduce the RESP charges, but obviously (sqm is semi-empirical method, not like gaussian) it won't be accurate. However, you're right, if you have the RESP charges in prep.ch3cn just copy them by hand accordingly. Or even better, if you want to learn more about the whole stuff, double check if the parameters you got from the Manchester site are OK, why not trying q4md-forcefieldtools.org/RED/? Once you got the charges (they should be very close if not the same from prep.ch3cn), you can use acpype just to generate the topology by providing a c3n.MOL2 file with the charges calculated by RED and then using acpype -di c3n.mol2 -c user. 2) dummy atoms as listed in the prep.ch3cn are not present in the new .itp file. I guess you don't know how a prep file works, so see http://ambermd.org/doc/prep.html. 3) the force constants seem totally different. shall i again just adjust them to the original file obtained from the amber site? If using acpype with default mode, so you'd get GAFF parameters. You may want to try: acpype -di c3n.mol2 -c user -a amber However, it still may diff. If you read Jaime's paper and you agree with what he did, so you can copypaste his parameters as well. is there another way of using acpype, with a proper args list, that i should use in this situation? Read the Wikis in the acpype site and 'acpype -h'. I am always keen for suggestions. Another possible way, would be using tleap from AmberTools, generate just one molecule, save parameters and use acpype to convert from amber to gromacs, something like acpype -p c3n.prmtop -x c3n.inpcrd If doing so, you'd get the exactly Jaime's topology but in gromacs format (gro and top file, not itp, so you may need to adjust things in the top file in order to create a itp, but should be a simple task). BTW, how did you get this message cannot find template for residue C3N in our library? i got that message *within* the following output when running: acpype -i ch3cn_210.pdb [...] Warning: cannot find template for residue C3N in our library. You will not be able to save prmtop for this molecule. Warning: cannot find template for residue C3N in our library. You will not be able to save prmtop for this molecule. [gtkleap]$ #check C3N [gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd Error: dparm pchg does not exist! ++end_quote+ ERROR: Sleap failed == Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd' Total time of execution: 7s Ah, ok, I should've know this... It's a fall back routine to try to use 'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately. Thanks for trying acpype. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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: OPLS-AA/L force field
Dear Oliver, On Thu, May 20, 2010 at 13:21, gmx-users-requ...@gromacs.org wrote: I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies for the confusion! If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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] Re: OPLS-AA/L force field
*If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. *Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only problem is the NAc groups aren't restrained properly so have to manually edit them in. I'll have to do some reading about acpype... On 20 May 2010 13:28, Alan alanwil...@gmail.com wrote: Dear Oliver, On Thu, May 20, 2010 at 13:21, gmx-users-requ...@gromacs.org wrote: I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies for the confusion! If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- 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] enegry minimisation
Hello Gaurav, when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02. -- Sonali Dhindwal --- On Thu, 20/5/10, Gaurav Goel gauravgoel...@gmail.com wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, 20 May, 2010, 5:36 PM Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul jalem...@vt.edu wrote: sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title= protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist= 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol= 1000.0 emstep = 0.01 pbc= xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. Well, you haven't properly defined position restraints. The default (produced by pdb2gmx) requires define = -DPOSRES not -DPOSRE. If you have for some reason modified the topology, then maybe your approach is correct, but otherwise your position restraints are not being applied. I also find it very curious that such substantial changes are taking place during a simple energy minimization. Are you sure the effects you are seeing are not simply due to the visualization software you are using guessing the incorrect secondary structure type? I have had that experience numerous times, especially in the case of beta-strands. DSSP tells me that, geometrically, I have beta-strands, but the visualization software renders coil structures. In any case, large structural deviations during EM suggest something fundamentally wrong with the model. Usually the changes in EM are small, since it is performed at 0 K. Only huge forces would cause any sort of structural change. I also want to ask what is the meaning of fx fy and fz : Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 1 1000 1000 1000 23 1 1000 1000 1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? These default values are typically quite sufficient to restrain the structure. -Justin Thanks in advance. -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: sonali dhindwal sonali11dhind...@yahoo.co.in Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ... _ 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual. 2. Add define = -Dname to your mdp file 3. Add following lines to your topology file ; Include Position restraint file #ifdef name #include name.itp #endif 4. compile and run. I'm sure you will find mroe information on position-restrain simulation on gmx-users archive. -Gaurav On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal sonali11dhind...@yahoo.co.in /mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Hello Gaurav, Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then
Re: [gmx-users] enegry minimisation
sonali dhindwal wrote: Hello Gaurav, when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02. Is that backbone RMSD or does it consider all protein atoms? In either case, a value of 0.02 indicates a very small amount of change in the protein structure, which makes it very hard to believe that any large-scale alteration of the secondary structure is happening. -Justin -- Sonali Dhindwal --- On *Thu, 20/5/10, Gaurav Goel /gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, 20 May, 2010, 5:36 PM Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul jalem...@vt.edu /mc/compose?to=jalem...@vt.edu wrote: sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title = protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 pbc = xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. Well, you haven't properly defined position restraints. The default (produced by pdb2gmx) requires define = -DPOSRES not -DPOSRE. If you have for some reason modified the topology, then maybe your approach is correct, but otherwise your position restraints are not being applied. I also find it very curious that such substantial changes are taking place during a simple energy minimization. Are you sure the effects you are seeing are not simply due to the visualization software you are using guessing the incorrect secondary structure type? I have had that experience numerous times, especially in the case of beta-strands. DSSP tells me that, geometrically, I have beta-strands, but the visualization software renders coil structures. In any case, large structural deviations during EM suggest something fundamentally wrong with the model. Usually the changes in EM are small, since it is performed at 0 K. Only huge forces would cause any sort of structural change. I also want to ask what is the meaning of fx fy and fz : Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 1 1000 1000 1000 23 1 1000 1000 1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? These default values are typically quite sufficient to restrain the structure. -Justin Thanks in advance. -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: sonali dhindwal sonali11dhind...@yahoo.co.in /mc/compose?to=sonali11dhind...@yahoo.co.in Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ...
Re: [gmx-users] enegry minimisation
sonali dhindwal wrote: Thanks for your reply Justin, this is rms for protein backbone, it is showing as 0.02 but when i check it in pymol by aligning two molecules rms is 0.256, and there is change in the structre of the protein. Sounds like that's the same result (potentially). Gromacs uses nm for RMSD, maybe PyMOL uses Angstrom? Can you render an image and post it? I can't really grasp what's happening without seeing it. EM should not be making large changes to your structure, and a backbone RMSD of 0.02 nm does not sound like enough to cause serious distortion. Instructions for sharing the image (should you choose to provide it) can be found here (bullet point #4): http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin Regards -- Sonali Dhindwal --- On *Thu, 20/5/10, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, 20 May, 2010, 6:46 PM sonali dhindwal wrote: Hello Gaurav, when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02. Is that backbone RMSD or does it consider all protein atoms? In either case, a value of 0.02 indicates a very small amount of change in the protein structure, which makes it very hard to believe that any large-scale alteration of the secondary structure is happening. -Justin -- Sonali Dhindwal --- On *Thu, 20/5/10, Gaurav Goel /gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: jalem...@vt.edu /mc/compose?to=jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org Date: Thursday, 20 May, 2010, 5:36 PM Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul jalem...@vt.edu /mc/compose?to=jalem...@vt.edu /mc/compose?to=jalem...@vt.edu /mc/compose?to=jalem...@vt.edu wrote: sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title = protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 pbc = xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. Well, you haven't properly defined position restraints. The default (produced by pdb2gmx) requires define = -DPOSRES not -DPOSRE. If you have for some reason modified the topology, then maybe your approach is correct, but otherwise your position restraints are not being applied. I also find it very curious that such substantial changes are taking place during a simple energy minimization. Are you sure the effects you are seeing are not simply due to the visualization software you are using guessing the incorrect secondary structure type? I have had that experience numerous times, especially in the case of beta-strands. DSSP tells me that, geometrically, I have beta-strands, but the visualization software renders coil structures. In any case, large structural deviations during EM suggest something fundamentally wrong with the model. Usually the changes in EM are small, since it is performed at 0 K. Only huge
[gmx-users] PCA
I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows: 1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix? 2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened the eigenval.xvg file it will shows nothing, i don't know what was wrong with it? 3. what is the difference between covariance matrix and normal mode analysis because both were used to generate the eigenval.xvg and eigenvec.trr file? 4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the structures generated at the time of simulations of single structure without using the other structure? I mean to say that it is possible to use single structure as initial to simulate and ED sampling? 5. what is the need of eigenvec2.trr input file in g_anaeig to generate the single number of covariance matrix as shown in manual? I have used to input only one eigenvec.trr and eigenval.xvg, then it is right to do this? 6. I have used eigenval.xvg as input file in g_anaeig which do not shows nothing when used to open in xmgrace. Then how this file used for generating eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have successfully generated). 7. One last question is related to g_analyze that it reads ascii file and analyze data sets, but in actual it used some graph.xvg file as input. I am confused about this graph.xvg file which file should I used for input to calculate the cosine content of the principal components. -- Pawan -- 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] graphite and pi density
Hello, I want to put charge (as pi density) on each carbon atom at 1 A top and below of each carbon atom of graphaite sheet. Basically I want put a atom, X, with charge -0.5 and mass 0 at 0.5 A below and above the carbon atom. How can I do this? Thanks Nilesh -- 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: g_densmap
Dear Mark I used this sequence to obtain the gro file (gro reference in the next calculations) g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ Select a group for determining the system size: Group 0 ( System) has 6370 elements Group 1 ( HEME) has47 elements Group 2 ( SOL) has 6321 elements Group 3 ( NA+) has 2 elements Group 4 ( NA) has 1 elements Group 5 ( NC) has 1 elements Group 6 ( CHB) has 1 elements Group 7 ( CHD) has 1 elements Group 8 ( CHB-CHD) has 2 elements Group 9 ( Carb_ring) has 4 elements Group10 ( CHC) has 1 elements Group11 ( CHA) has 1 elements Group12 ( nitrog) has 3 elements Group13 ( ow_teste) has 1 elements Group14 ( HW1_HW2) has 4214 elements Group15 ( OW) has 2107 elements Group16 ( Fe) has 1 elements Select a group: 0 Selected 0: 'System' system size : 5.486 5.648 6.394 (nm) center : 3.463 3.499 1.671 (nm) box vectors : 4.471 4.471 4.563 (nm) box angles : 60.66 60.66 90.00 (degrees) box volume : 65.78 (nm^3) Select group for the determining the orientation Group 0 ( System) has 6370 elements Group 1 ( HEME) has47 elements Group 2 ( SOL) has 6321 elements Group 3 ( NA+) has 2 elements Group 4 ( NA) has 1 elements Group 5 ( NC) has 1 elements Group 6 ( CHB) has 1 elements Group 7 ( CHD) has 1 elements Group 8 ( CHB-CHD) has 2 elements Group 9 ( Carb_ring) has 4 elements Group10 ( CHC) has 1 elements Group11 ( CHA) has 1 elements Group12 ( nitrog) has 3 elements Group13 ( ow_teste) has 1 elements Group14 ( HW1_HW2) has 4214 elements Group15 ( OW) has 2107 elements Group16 ( Fe) has 1 elements Select a group: 8 Selected 8: 'CHB-CHD' new system size : 5.486 5.648 6.394 shift : -0.110 -0.145 -0.026 (nm) new center : 3.353 3.353 1.645 (nm) new box vectors : 4.471 4.471 4.563 (nm) new box angles : 60.66 60.66 90.00 (degrees) new box volume : 65.78 (nm^3) Select a group for output: Group 0 ( System) has 6370 elements Group 1 ( HEME) has47 elements Group 2 ( SOL) has 6321 elements Group 3 ( NA+) has 2 elements Group 4 ( NA) has 1 elements Group 5 ( NC) has 1 elements Group 6 ( CHB) has 1 elements Group 7 ( CHD) has 1 elements Group 8 ( CHB-CHD) has 2 elements Group 9 ( Carb_ring) has 4 elements Group10 ( CHC) has 1 elements Group11 ( CHA) has 1 elements Group12 ( nitrog) has 3 elements Group13 ( ow_teste) has 1 elements Group14 ( HW1_HW2) has 4214 elements Group15 ( OW) has 2107 elements Group16 ( Fe) has 1 elements Select a group: 0 Selected 0: 'System' where CHB-CHD (molecular axis) must to coincide with the axis (X or Y). My molecule is well centered and the box axis coincide with the molecular axis (chosen according to my interest) The results are similar to make it in two steps (1) g_densmap_d -f tmp-prueba.gro -n index.ndx -o tmp_prueba1.gro -princ(2) g_densmap_d -f tmp-prueba1.gro -n index.ndx -o tmp_prueba2.gro -c The molecule was centered in every step simulation. trjconv_mpi_d -s heme_centered.tpr -f dm10nsheme.xtc -o dm10nsheme_cent.xtc -center -boxcenter rect -pbc mol The box was rotate to XY plane concide with the XY molecular plane in every step simulation trjconv_mpi_d -s tmp_prueba2.gro -f dm10nsheme_cent.xtc -o dm10nsppix_cent_norotTrans.xtc -fit rot+trans To obtain the XY density map g_densmap_mpi_d -f m10nsppix_cent_norotTrans.xtc -s tmp_prueba2.gro -n index.ndx -o tmpdensmaphemeXY.xpm when I applied the g_densmap tool, there is not difference with my previous result. In the density map, my molecule appear in the corner, and white diffuse regions (maybe by the box rotations) appear. I think the problem will be the way that I eliminate the rotations and translations. But I don't have a clear idea of what I've done wrong Regards Ricardo .. Please use a descriptive subject line to help everybody. I suspect
[gmx-users] Re: graphite and pi density
I want to put charge (as pi density) on each carbon atom at 1 A top and below of each carbon atom of graphaite sheet. Basically I want put a atom, X, with charge -0.5 and mass 0 at 0.5 A below and above the carbon atom. How can I do this? Thanks Nilesh Hi Nilesh, Looks interesting. How did you estimate this charge of -0.5 ? Dummy atoms in gromacs should be useful to do what you want. ~Vitaly -- Dr. Vitaly Chaban -- 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] mdrun segmentation fault
Hi I have gromacs input files for md simulation, with these set up files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one machine, but when I move it to other machine, I get segmentation fault when I do mdrun. Both the machines have exactly same types of installation of gromacs 4.0.7 . Also, I can run water tutorials successfully on both the machines. So what could be the source of segmentation fault? thanks sikandar -- 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] mdrun segmentation fault
Sikandar Mashayak wrote: Hi I have gromacs input files for md simulation, with these set up files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one machine, but when I move it to other machine, I get segmentation fault when I do mdrun. Both the machines have exactly same types of installation of gromacs 4.0.7 . Also, I can run water tutorials successfully on both the machines. So what could be the source of segmentation fault? MD is chaotic, so you may not get the same result every time you run a simulation. Since you've not said how quickly the seg fault occurs it is exceptionally hard to diagnose. Generally, seg faults with mdrun occur because the system crashes from an instability. Without substantially more information (system contents, .mdp settings, relevant log file output, etc) there is not much more to suggest. -Justin thanks sikandar -- 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
Re: [gmx-users] mdrun segmentation fault
It happens immediately at step 0., and the log file looks like :
Input Parameters:
integrator = md
nsteps = 2
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode= Linear
nstlog = 1000
nstxout = 600
nstvout = 600
nstfout = 600
nstenergy= 1000
nstxtcout= 1000
init_t = 0
delta_t = 0.001
xtcprec = 1
nkx = 44
nky = 42
nkz = 120
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 1
epsilon_surface = -1
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 100
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 0 12822
ref_t: 0 300
tau_t: 0 0.2
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: Y Y Y N
N N
energygrp_flags[ 0]: 1 0
energygrp_flags[ 1]: 0 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
PLEASE READ AND CITE THE FOLLOWING REFERENCE
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995)
Re: [gmx-users] mdrun segmentation fault
Sikandar Mashayak wrote:
It happens immediately at step 0., and the log file looks like :
That suggests to me that the system is inherently unstable, which can occur for
a variety of reasons.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
A few more comments below.
Input Parameters:
integrator = md
nsteps = 2
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode= Linear
nstlog = 1000
nstxout = 600
nstvout = 600
nstfout = 600
nstenergy= 1000
nstxtcout= 1000
init_t = 0
delta_t = 0.001
xtcprec = 1
nkx = 44
nky = 42
nkz = 120
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 1
epsilon_surface = -1
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Nose-Hoover
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 100
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 0 12822
ref_t: 0 300
tau_t: 0 0.2
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: Y Y Y N
N N
energygrp_flags[ 0]: 1 0
energygrp_flags[ 1]: 0 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw:
[gmx-users] polymer simulation
Dear all, I would like to know that is there any gromacs tool which can generate a polymer melt? If not, is there any tool you can suggest which can do the job. Thank you. Sudip -- ** Dr. Sudip Roy Physical Chemistry and Material Science Division Scientist C National Chemical Laboratory Pune 411008 India Tel. +91 2590 2735 Office Email s@ncl.res.in Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/common/webmailDisclaimer.htm -- 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] confusion about segmentation fault during mdrun
Hi Justin, I took all your suggestions. But the same thing happened again in the NPT step with the Segmentation fault for some starting structure. I attached the mdp file I used. Do you have any idea what else could cause this error? Thank you very much! Best, Lan On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Lan Hua wrote: Hi Justin, I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right? Maybe. If your goal is REMD (I'm not clear from your original post) then stability may be an issue at higher temperatures, in which case you may need to constrain all bonds or decrease your time step, maybe both. At ambient temperatures, what you propose is likely stable. Look into the relevant literature for similar force fields and applications to be sure. -Justin Thanks, Lan On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Lan Hua wrote: Hi Justin, Thank you so much for your quick reply and good suggestions. The following is my answer. On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Lan Hua wrote: Hi All, I understand that the error of segmentation fault may come from many reasons, but I just couldn't figure out the reason of this error in my simulations. I want to run md simulations with explicit water for 20 structures of one domain (residue 77-148) of calmodulin (PDB 1CFC). These 20 starting structures are from one REMD simulation in implicit water. The following is what I did to run simulations for these 20 structures. I used gromacs version 3.1.4 with ffamber ports. The force field is amber03 and water model is TIP3P. Do you have any particular reason for using software that is eight years old? You will get a massive performance upgrade with 4.0.7, as well as the ability to use multiple processors per replica. In versions prior to 4.0, you can only use one processor per REMD replica. The reason that I am using gromacs 3.1.4 is to prepare some input files for simulations at fold...@home in which version 3.1.4 is recommended. OK, as long as you've got a reason... 1. get rid of the steric clash in the starting structure What do you mean? Energy minimization? How did you did do this prior to step 2 (generating a topology)? I used the protein preparation wizard which is implemented in maestro package to do this. Actually in this wizard, energy minimization is performed on protein. 2. after doing pdb2gmx, then minimze the protein 3, use -bt dodecahedron -d 0.9 -c in the command line of editconf 4, after doing genbox, first minimize the water with protein rigid and then minimize the whole system A lot of these steps are redundant and probably unnecessary. Some tips: http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation Thanks for the tips. I went to the link, but I am still a little bit confused about which steps are unnecessary. You mean step 7 and step 8? I did this in case simulations at f...@h would be crashed. I just mean the repeated, separate energy minimizations. I guess there's no harm in it, but generally I find that minimizing the protein in vacuo, then with and without restraints in solvent, etc. is unnecessary. I'd suggest just building the system (solvent and all), and minimizing the whole thing (without restraints). I don't think you stand to gain anything with your procedure. 5, run md simulation with position restraint for protein heavy atoms with nose-hoover thermostat for 20ps 6, run NPT simulations with nose-hoover thermostat and Parrinello-Rahman thermostat for 500ps 7, run NVT simulation for another 100ps 8, then energy minimze the whole system again. Every time, there are always segmentation fault in step 6 for some starting structures which could be different in every try. I checked the energy, volume, pressure, temperature, etc for the trajectories which are crashed because of segmentation fault, but nothing was wrong. I roughly checked
Re: [gmx-users] confusion about segmentation fault during mdrun
Lan Hua wrote: Hi Justin, I took all your suggestions. But the same thing happened again in the NPT step with the Segmentation fault for some starting structure. I attached the mdp file I used. Do you have any idea what else could cause this error? Thank you very much! The only advice I can give is here (with special attention to the Diagnosing an Unstable System section): http://www.gromacs.org/Documentation/Terminology/Blowing_Up I know you have explained your reasoning for using version 3.1.4, but do realize that there have been numerous bug fixes and feature upgrades in the last 8 (yikes!) years of Gromacs development that may affect stability. I have never used 3.1.4, so if there's some inherent issue with that version, you can also check the list archive for anyone that had similar issues back when 3.1.4 was actually a recent release. -Justin -- 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
RE: [gmx-users] polymer simulation
If you are referring to something that will generate a coordinate file (.pdb or .gro) of polymer molecules randomly distributed, then there is not currently a script with GROMACS that will do that job. If you have a single molecule, there are a couple of tools that can randomly spread those molecules around, though not very well. 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] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- 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] enegry minimisation
hello Jusitn, Thanks for your reply,, I am sending you the link, so that you can see the changes in the protein, I have specifically shown that part of the protein, where I am seeing changes, http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink Yello beeta sheets are of the protein after EM, and magenta are that of the refrence structure, you can see how this time,I am surprised myself that sheets have become longer than the refrence structure. I have corrected that define = -DPOSRES also. and have taken that posres file generated by pdb2gmx.is this the problem of the visualiser I m using, I am using pymol for it Thanks -- Sonali Dhindwal -- 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
