[gmx-users] R: gmx-users Digest, Vol 82, Issue 113
Tsjerk, sure, I meant exactly what you are saying, by my english is not as good as yours... Thank you again Anna -- Message: 1 Date: Mon, 14 Feb 2011 17:36:27 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] R: visualizing more than residues... To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTi=PB=SJMJVKNxB75zAzZMYM7CPmiuH=fravp...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, I didn't say the PDB format does not allow more than residues. It does. But it does not allow numbers higher than . Thus, with more residues, it will start counting over. Cheers, Tsjerk On Mon, Feb 14, 2011 at 4:52 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear Tsjerk, thank you very much. I really didn't know that the PDB format does not allow more than residues (in fact, it is the first time I have such a big system to manage). I will follow your suggestions trying to solve the problem with chain identifiers. Many thanks and best regards Anna -- Message: 6 Date: Mon, 14 Feb 2011 16:43:29 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] visualizing more than residues To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: AANLkTikVM8kt1F5p3=4o9s9kjdgvvk-pxkznro6an...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, The 'problem' is the PDB file format. It is a fixed-width format that does not allow for residue numbers with more than 4 digits. Both VMD and PyMOL do not have problems reading structures with more residues, but they will choke if you renumber the residues, giving numbers with five or more digits. It breaks the file format. It may be a bit troublesome making selections if you have ambiguous residue identifiers, but that's the way it is with PDB files. You can try to be creative with chain identifiers and segment identifiers to give all residues unique markers. Cheers, Tsjerk On Mon, Feb 14, 2011 at 4:29 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I have a system formed by protein+ligand+lipid bilayer that accounts for about 10500 residues (56000 atoms). It seems to me that it is not possible to visualize correctly such a large system with Pymol or VMD, because it seems that the max number of residues that I can manage with both programs is exactly . Moreover, it's not only a visualization problem, since I also had several problems trying to use Pymol or VMD to create the system in which the protein+ligand is correctly oriented with respect to the lipid bilayer, to proceed further with g_membed. I had several problems in saving the .pdb file (after the th residue, the numbering restarted from 0; when I manually corrected this prroblem and re-numbered the file, I opened it with VMD and Python and found some aberrant visualization of the water molecules exceeding the number of . At last, I decided to remove the exceeding waters). I know that this is a Gromacs user list, not a Pymol or VMD user list, but since it seems to me that these two programs are generally considered as a graphical interface with respect to Gromacs, I'd like to know how you folks manage this problem without removing residues. I searched for some hints in the gmx-user list and in Google but I didn't find anything. Thank you very much and sorry for this off-topic question. Anna Marabotti __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
[gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
Hi all, first I would like to thank Justin A. Lemkul for the tutorials provided which are very helpful for new users like me. I am doing a membrane protein simulation and now doing packing of the lipids around the protein. I had run the inflategro.pl script and and now I am facing a problem doing energy minimization of my inflated system (contatining protein and the lipid membrane) using grompp. I have updated my topology file accordingly ie removed the spc.itp, ions.itp it now only contains protein and dppc the protein is of 3881 atoms but after updating my topolgy it still gives the following error: Fatal error: number of coordinates in coordinate file (system_inflated.gro, 9331) does not match topology (topol.top, 10281) As i understand it could be because of the deleted lipids of the system, if so how can I know the deleted number of lipids. My topology file looks like - ; ; This is your topology file ; protein ; ; Include forcefield parameters #include ffG53a6_lipid.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] . . . . ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DPPC chain topology #include dppc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound#mols Protein_A 1 DPPC128 thank you, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ffamber03 top file problem
Dear All: I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter. I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate: --- Program grompp_m, VERSION 4.5.1 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROM··· I added some bonds and angles parameters like this: ·· ; residue 44 ASN rtp ASN q 0.0 664 N 44ASN N664 -0.430106 14.01 ; qtot 4.57 665 HD44ASN HD665 0.250466 2.016 ; qtot 4.824 666 CT 44ASN CA666 0.044609 12.01 ; qtot 4.869 ··· [ bonds ] ; aiaj functc0c1c2c3 ··· 676 678 1 678 679 1 0.10115 678 680 1 680 681 1 ··· [ angles ] ; aiajak functc0c1c2c3 648 650 652 1 651 650 652 1 115.149 650 652 653 1 650 652 654 1 Any help will highly appreciated!-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
On Tue, Feb 15, 2011 at 5:25 PM, Parul tew parul...@gmail.com wrote: Hi all, first I would like to thank Justin A. Lemkul for the tutorials provided which are very helpful for new users like me. I am doing a membrane protein simulation and now doing packing of the lipids around the protein. I had run the inflategro.pl script and and now I am facing a problem doing energy minimization of my inflated system (contatining protein and the lipid membrane) using grompp. I have updated my topology file accordingly ie removed the spc.itp, ions.itp it now only contains protein and dppc the protein is of 3881 atoms but after updating my topolgy it still gives the following error: Fatal error: number of coordinates in coordinate file (system_inflated.gro, 9331) does not match topology (topol.top, 10281) As i understand it could be because of the deleted lipids of the system, if so how can I know the deleted number of lipids. My topology file looks like - ; ; This is your topology file ; protein ; ; Include forcefield parameters #include ffG53a6_lipid.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] . . . . ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DPPC chain topology #include dppc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound#mols Protein_A 1 DPPC128 After insertion, there are probably several DPPC molecules removed. Check outputs from inflategro.pl, then update accordingly. Terry thank you, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and 4.5.2 version
Justin A. Lemkul skrev 2011-02-09 23.03: Zuzana Benkova wrote: Dear GROMACS users, I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance. Try pulling the latest stable development version. This issue was reported in 4.5.1: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html but not fixed until after 4.5.3 was released: http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html -Justin Greetings Zuzana Are people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ffamber03 top file problem
Check the topology section in the gromacs manual. You'll find the format you should use for bonds, angles etc.On 15-02-11, gromacs564 gromacs...@126.com wrote:Dear All: I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter. I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate:---Program grompp_m, VERSION 4.5.1Source code file: toppush.c, line: 1631Fatal error:Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For more information and tips for troubleshooting, please check the GROM···I added some bonds and angles parameters like this:··; residue 44 ASN rtp ASN q 0.0 664 N 44 ASN N 664 -0.430106 14.01 ; qtot 4.57 665 HD 44 ASN HD 665 0.250466 2.016 ; qtot 4.824 666 CT 44 ASN CA 666 0.044609 12.01 ; qtot 4.869···[ bonds ]; ai aj funct c0 c1 c2 c3··· 676 678 1 678 679 1 0.10115 678 680 1 680 681 1 ···[ angles ]; ai aj ak funct c0 c1 c2 c3 648 650 652 1 651 650 652 1 115.149 650 652 653 1 650 652 654 1 Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Whereabouts of NDLP???
Hi, Was this server ever reestablished? Is there a link which I can use to calculate the optimal box? Thanks, Ifat* * Hi Alan, Unfortunately there have been server problems (severe hacking) in Groningen some while ago, and the NDLP server was terminated. But, we're right about to reestablish an improved server here in Utrecht. This server will be much faster, seconds rather than hours - the optimal packing for the GroEL/GroES complex (60k atoms) took somewhere around a minute maybe, and will also provide an optimal simulation cell for a given ensemble (NMR, ENM, MD). In addition, the principal author at the time was not in favour of adding the program to the Gromacs suite, and there were some depency issues as well. I don't see why the new program should not also become incorporated in Gromacs. That being said, we still need a bit of time here to wrap things up. In the mean time, as long as I'm not run over by requests, you can send me a (few) structure(s) off the list, and I'll be happy to calculate the packing. Best, Tsjerk On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen achen at artsci.wustl.eduhttp://www.gromacs.org/mailman/listinfo/gmx-users wrote: * Hi All: ** ** I recently came across Tsjerk Wassenaar's JCC papers about a ** Near-Densest Lattice Packing ** algorithm for choosing the optimal triclinic box for a non-spherical ** macromolecule. ** http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html ** ** I have a rather cylindrical RNA I am studying right now, and I wanted ** to try out NDLP only the website referred to by the paper ** no longer exists, and I can't find any reference to NDLP on the new ** rug.nl homepage nor does google give me any clues. Does ** anyone know as to this package's current whereabouts? ** ** Thanks, ** Alan Chen ** ** ** ___ ** gmx-users mailing listgmx-users at gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users ** http://www.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-request at gromacs.org.http://www.gromacs.org/mailman/listinfo/gmx-users ** Can't post? Read http://www.gromacs.org/mailing_lists/users.php ** * -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Whereabouts of NDLP???
Hi Ifat, It has: http://haddock.chem.uu.nl/Squeeze/ Cheers, Tsjerk On Tue, Feb 15, 2011 at 12:46 PM, ifat shub shubi...@gmail.com wrote: Hi, Was this server ever reestablished? Is there a link which I can use to calculate the optimal box? Thanks, Ifat Hi Alan, Unfortunately there have been server problems (severe hacking) in Groningen some while ago, and the NDLP server was terminated. But, we're right about to reestablish an improved server here in Utrecht. This server will be much faster, seconds rather than hours - the optimal packing for the GroEL/GroES complex (60k atoms) took somewhere around a minute maybe, and will also provide an optimal simulation cell for a given ensemble (NMR, ENM, MD). In addition, the principal author at the time was not in favour of adding the program to the Gromacs suite, and there were some depency issues as well. I don't see why the new program should not also become incorporated in Gromacs. That being said, we still need a bit of time here to wrap things up. In the mean time, as long as I'm not run over by requests, you can send me a (few) structure(s) off the list, and I'll be happy to calculate the packing. Best, Tsjerk On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen achen at artsci.wustl.edu wrote: Hi All: I recently came across Tsjerk Wassenaar's JCC papers about a Near-Densest Lattice Packing algorithm for choosing the optimal triclinic box for a non-spherical macromolecule. http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html I have a rather cylindrical RNA I am studying right now, and I wanted to try out NDLP only the website referred to by the paper no longer exists, and I can't find any reference to NDLP on the new rug.nl homepage nor does google give me any clues. Does anyone know as to this package's current whereabouts? Thanks, Alan Chen ___ gmx-users mailing list gmx-users at gromacs.org http://www.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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and 4.5.2 version
Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund er...@xray.bmc.uu.se wrote:Justin A. Lemkul skrev 2011-02-09 23.03:Zuzana Benkova wrote:Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond.However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2.I would appreciate any help. Thank you in advance.Try pulling the latest stable development version. This issue was reported in 4.5.1:http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.htmlbut not fixed until after 4.5.3 was released:http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html-JustinGreetingsZuzanaAre people who are reporting this error using a triclinic boxes or cuboid boxes. That information may help my bugfixing.-- ---Erik Marklund, PhD studentDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole
Hello, I want to calculate dipole autocorrelation function without normalization. How can I calculate dipole autocorrelation function without normalization. I am using gromacs 4.0.7 version. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole
On 2011-02-15 13.51, Nilesh Dhumal wrote: Hello, I want to calculate dipole autocorrelation function without normalization. How can I calculate dipole autocorrelation function without normalization. I am using gromacs 4.0.7 version. Thanks Nilesh g_dipoles -h -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole
I used following command. g_dipoles -f 6.trr -s 6.tpr -corr total -normalize NO -c Its not working. Its giving following error Invalid command line argument: NO Nilesh On Tue, February 15, 2011 7:57 am, David van der Spoel wrote: On 2011-02-15 13.51, Nilesh Dhumal wrote: Hello, I want to calculate dipole autocorrelation function without normalization. How can I calculate dipole autocorrelation function without normalization. I am using gromacs 4.0.7 version. Thanks Nilesh g_dipoles -h -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole
Nilesh Dhumal wrote: I used following command. g_dipoles -f 6.trr -s 6.tpr -corr total -normalize NO -c Its not working. Its giving following error Invalid command line argument: NO With arguments listed as -[no]option, the proper argument is -nooption so in your case, -nonormalize. -Justin Nilesh On Tue, February 15, 2011 7:57 am, David van der Spoel wrote: On 2011-02-15 13.51, Nilesh Dhumal wrote: Hello, I want to calculate dipole autocorrelation function without normalization. How can I calculate dipole autocorrelation function without normalization. I am using gromacs 4.0.7 version. Thanks Nilesh g_dipoles -h -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NVE simulation
Hello! Is it possible to run NVE simulations insteed of NVT or NPT in Gromacs? Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVE simulation
Thomas Koller wrote: Hello! Is it possible to run NVE simulations insteed of NVT or NPT in Gromacs? Yes. http://www.gromacs.org/Documentation/Terminology/NVE -Justin Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella sampling windows
Hi all, I'm running umbrella sampling of an ion through a lipid bilayer with gromacs 4.5.1. I used g_wham to create the histograms of the configurations within the umbrella sampling windows (1 Angstrom interval). I did not get a sufficient overlap between the windows, so I was wodering which is the better way of increasing the sampling: to include additional windows in the regions where there is no overlap or to increase the force constant ? If I increase the force constant can I continue the simulation with the new constant or do I have to start again? I used a force contant of 3000 kJ mol^-1 nm^-2. Thank you in advance, Susana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling windows
Susana Tomasio wrote: Hi all, I'm running umbrella sampling of an ion through a lipid bilayer with gromacs 4.5.1. I used g_wham to create the histograms of the configurations within the umbrella sampling windows (1 Angstrom interval). I did not get a sufficient overlap between the windows, so I was wodering which is the better way of increasing the sampling: to include additional windows in the regions where there is no overlap or to increase the force constant ? If you increase the force constant, you will make the distributions narrower, and thus I would expect the overlap would be worse. Insufficient simulation length could be an issue, too, but you haven't said how long your simulations are. If I increase the force constant can I continue the simulation with the new constant or do I have to start again? You'd have to start over again, I'd think, otherwise if you pass one .tpr file to g_wham per window, it will contain incorrect information that will mess up the calculations. I used a force contant of 3000 kJ mol^-1 nm^-2. That seems somewhat high, but there are no hard and fast rules about these things, I don't think. You probably want either (1) a lower force constant or (2) more windows along your reaction coordinate. Option (2) seems to be more efficient, since you don't have to re-do your simulations, you can just run some more. -Justin Thank you in advance, Susana -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling windows
Hello Susana, I agree with Justin, 3000 kj/molnm2 seems pretty high. I've been using about a 1000kj/molnm2 force constant with window separation of about 0.8, that seems to work well for my system. -Laura On 02/15/2011 09:51 AM, Susana Tomasio wrote: Hi all, I'm running umbrella sampling of an ion through a lipid bilayer with gromacs 4.5.1. I used g_wham to create the histograms of the configurations within the umbrella sampling windows (1 Angstrom interval). I did not get a sufficient overlap between the windows, so I was wodering which is the better way of increasing the sampling: to include additional windows in the regions where there is no overlap or to increase the force constant ? If I increase the force constant can I continue the simulation with the new constant or do I have to start again? I used a force contant of 3000 kJ mol^-1 nm^-2. Thank you in advance, Susana -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling windows
Thank you very much for your help. I've run my simulations for 80 ns. I will add more windows along the reaction coordinate. Thank you, Susana On Tue, Feb 15, 2011 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Susana Tomasio wrote: Hi all, I'm running umbrella sampling of an ion through a lipid bilayer with gromacs 4.5.1. I used g_wham to create the histograms of the configurations within the umbrella sampling windows (1 Angstrom interval). I did not get a sufficient overlap between the windows, so I was wodering which is the better way of increasing the sampling: to include additional windows in the regions where there is no overlap or to increase the force constant ? If you increase the force constant, you will make the distributions narrower, and thus I would expect the overlap would be worse. Insufficient simulation length could be an issue, too, but you haven't said how long your simulations are. If I increase the force constant can I continue the simulation with the new constant or do I have to start again? You'd have to start over again, I'd think, otherwise if you pass one .tpr file to g_wham per window, it will contain incorrect information that will mess up the calculations. I used a force contant of 3000 kJ mol^-1 nm^-2. That seems somewhat high, but there are no hard and fast rules about these things, I don't think. You probably want either (1) a lower force constant or (2) more windows along your reaction coordinate. Option (2) seems to be more efficient, since you don't have to re-do your simulations, you can just run some more. -Justin Thank you in advance, Susana -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | +15402319080(540) 231-9080 +15402319080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling windows
Thank you very much for your help. I've run my simulations for 80 ns. I will add more windows along the reaction coordinate. Thank you, Susana On Tue, Feb 15, 2011 at 2:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Susana Tomasio wrote: Hi all, I'm running umbrella sampling of an ion through a lipid bilayer with gromacs 4.5.1. I used g_wham to create the histograms of the configurations within the umbrella sampling windows (1 Angstrom interval). I did not get a sufficient overlap between the windows, so I was wodering which is the better way of increasing the sampling: to include additional windows in the regions where there is no overlap or to increase the force constant ? If you increase the force constant, you will make the distributions narrower, and thus I would expect the overlap would be worse. Insufficient simulation length could be an issue, too, but you haven't said how long your simulations are. If I increase the force constant can I continue the simulation with the new constant or do I have to start again? You'd have to start over again, I'd think, otherwise if you pass one .tpr file to g_wham per window, it will contain incorrect information that will mess up the calculations. I used a force contant of 3000 kJ mol^-1 nm^-2. That seems somewhat high, but there are no hard and fast rules about these things, I don't think. You probably want either (1) a lower force constant or (2) more windows along your reaction coordinate. Option (2) seems to be more efficient, since you don't have to re-do your simulations, you can just run some more. -Justin Thank you in advance, Susana -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | +15402319080(540) 231-9080 +15402319080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein
Hello, While trying to visualize a MARTINI protein/trajectory in VMD, I came across the script top2psf.pl. i attempted to use it as: ./top2psf.pl -i martini.top -o martini.psf this generates the error: Cannot open atoms for reading: No such file or directory Anyone encounter this or have any suggestions for visualizing MARTINI proteins in VMD? Thank you for any help. -j -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein
John wrote: Hello, While trying to visualize a MARTINI protein/trajectory in VMD, I came across the script top2psf.pl http://top2psf.pl. i attempted to use it as: ./top2psf.pl http://top2psf.pl -i martini.top -o martini.psf this generates the error: Cannot open atoms for reading: No such file or directory Anyone encounter this or have any suggestions for visualizing MARTINI proteins in VMD? Thank you for any help. The required input is the actual protein topology (usually an #included .itp file within the .top). -Justin -j -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulation using Martini force field
regarding parameterization of phosphorylated serine I checked the Martini papers and I couldn't find how it is done. Can somebody please instruct me. In addition in JCTC paper from 2008 I saw that they simulated pentapeptides without imposing secondary structure. How can I do it? The problem is that there is no good tutorial how to use Martini (something general). If I still want to use Martini without imposing secondary structure how should I do it? What tutorial is better to use the one for lipids or the one for proteins in water. I think I should explain what exactly I want to do. I want to simulate casein protein that is natively unstructured. The only thing that is known about this protein that it creates micelles. I just want to see if it possible to create micelles with Martini and I'm trying to understand what is the better way to run Martini taking into consideration the limitations of the force field and my system. As I'm not an expert in Gromacs neither in Martini force field I will appreciate very much any help for setting this simulation. Thank you very much in advance. Regina n Feb 14, 2011, at 11:43 PM, pol...@fh.huji.ac.il wrote: Thank you very much for you reply. Can you please explain me why do i need secondary structure file at all and why secondary structure is pre-defined and thus static throughout a simulation? I didn't see that something like this defined for lipids. Have look at the Martini paper for protein (JCTC-2009) you might find some stuff quite instructive in there :)) FYI lipids do not have secondary structure or something that would succgest they could have different interacting behavior in function of their conformation. How do I use do_dssp to build the needed file? I saw that I need a topology file in rder to use do_dssp. Where can I find this topology file? I hope this is ok that I'm asking so many questions. Thank you very much for your help. No problem it just shows how it was a good idea to make a tutorial :)) have look there cgmartini.nl Regina Quoting XAvier Periole x.peri...@rug.nl: Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of coil for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini coil is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Advanced Simulation Analysis
Hi, I have been trying to follow the tutorial posted by David van der Spoel to generate the order parameters at: https://extras.csc.fi/chem/courses/gmx2007/analysis/index.html When I ran g_rotacf, I got the following message: Fatal error: Number of index elements not multiple of 2, these can not be atom doublet. Has anyone tried that tutorial? Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Advanced Simulation Analysis
On 2011-02-15 18.01, simon sham wrote: Hi, I have been trying to follow the tutorial posted by David van der Spoel to generate the order parameters at: https://extras.csc.fi/chem/courses/gmx2007/analysis/index.html When I ran g_rotacf, I got the following message: Fatal error: Number of index elements not multiple of 2, these can not be atom doublet. Has anyone tried that tutorial? Best, Simon Sham You need to specify a list of atom pairs, I guess N H N H etc. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: free energy
Moeed, Sorry for the late response, and yes I did need to include more information in my answer. 1) If your polymers are physically close together in reality you might want to have multiple polymers in a single FEP job. I run single ligands in proteins, so this has never been an issue. You may want to run both and see what the differences in energy are. If there are none you may be able to do longer md/sd runs with a smaller one polymer system than you could with multiple polymers in the same time. In other words I have no idea what your system will need. Sorry. 2) How many windows and how long are the md/sd runs for each window? I personally found that 21 windows works well for my systems. This however will vary by the dV/dlambda graph. If and when your dV/dlambda is changing more (ddV/dlambda) you will need more windows to get a more accurate energy. Most systems change the most at the beginning and end of lambda values. I run a lambda every 0.05, but my systems are huge! (100,000 atoms) 3) Bennett acceptance ratio is an extra step in setup but makes getting your data much easier to interpret. Once you are done with all your windows you run g_bar and it will print out on your screen the energy from each window and the total energy in kJ/mol with a standard deviation. This can be found in the manual and also in the gmx_user archives. This entailes making a .mdp file for every step (but you probably do this already) and setting the foreign lambdas correctly. ie for lambda values: 0.00, 0.25, 0.50, 0.75 and 1.00 Your foreign lambda values for the 0.00 mdp file would be: 0.25 Your foreign lambda values for the 0.25 mdp file would be: 0.00 0.50 Your foreign lambda values for the 0.50 mdp file would be: 0.25 0.75 Your foreign lambda values for the 0.75 mdp file would be: 0.50 1.00 Your foreign lambda values for the 0.50 mdp file would be: 0.75 This of course is a small number of lambda values you will want to use more. Please email me with questions if you need more. Thank you, TJ Mustard Email: musta...@onid.orst.edu PS more below On February 14, 2011 at 8:54 PM Moeed lecie...@googlemail.com wrote: Hello, Sorry but it seems you wanted to answer my question on gmx list but I dont see anything!... -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/ TJ Mustard Email: musta...@onid.orst.edu Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results? 2- I have switched off electrostatics so I am using free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no In David Mobleys turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +). This old tutorial is for an old gromacs which needs you to set the state a and state b. In the newer gromacs releases you set the state a, and gromacs will go to state b without you setting each atom. This considerably saves time making .itp files. All you need is a methane .itp file (got mine from antechamber) and then you set couple-lambda0 and couple-lambda1 to what you are looking for. I personally go from couple-lambda0 = vdw-q to couple-lambda1 = none. Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed TJ Mustard Email: musta...@onid.orst.edu
Re: [gmx-users] free energy
One other thing I would point out is that the solvation free energy is dependent on concentration. you will get a different result with 4 polymer chains vs 3 vs 3, etc. Make sure you understand the dependence. Also, the free energy will depend on the polymer chain length. Polymer and finite concentration calculations are harder to interpret than monomer and infinite dilution calculations. Make sure you understand the differences. I'm not sure understand all of them, though, so you'll have to think about it yourself! Basically, you need to make sure the physical picture of the molecules in gromacs is the physical picture of the realistic molecular system itself. On Mon, Feb 14, 2011 at 6:28 PM, Moeed lecie...@googlemail.com wrote: Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to have in my system. If FE can be done with only one chain, am I making system bigger in vain? Does this matter affect the accuracy of results? 2- I have switched off electrostatics so I am using free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no In David Mobley's turorial the last three lines are not included. I wanted to know if I am to run say 10 simulations for different lambda, what purpose does the last three lines serve in 4.0.7 ? I got very close values in that tutorial without these settings. ( I know what these lines mean, just curious how these three lines affect the results in 4 X +). Please let me know your comments/point of view about the system and setting I am using. Thanks Moeed -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
So, I installed the development package for x-window-system, and reinstalled both fftw, and gromacs, and now everything seems fine. I do see the animation after running demo. Thanks, Majid From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 9:39:12 PM Subject: Re: [gmx-users] Gromacs Installation On 15/02/2011 4:35 PM, majid hasan wrote: Okay, I'll do this. I have also realized after browsing through config.log, that Xlib.h is absent. Where do I get it, I want it to run ngmx. You will need the X windowing system installed, and probably the associated devel packages. Use your distribution's package manager. Mark Thanks, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 9:07:15 PM Subject: Re: [gmx-users] Gromacs Installation clean reinstallation. make uninstall make distclean rm -r the untar one from source re-install it again. lina On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.com wrote: Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one, I just ran the whole process again starting from fftw$./configure. I am not sure if that is all right, I just did it to find out the problem. In the third attempt (without issuing --enable-shared anywher), I again over-wrote the gromacs installation files, and this went well. It worked, but I don't know why? Best, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 8:04:38 PM Subject: Re: [gmx-users] Gromacs Installation You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina Food fight? Enjoy some healthy debate in the Yahoo! Answers Food Drink QA. No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Repulsion instead of adsorption
Dear all I'm working on simulation of adsorption on the sheet . I use periodic boundary conditions in two dimension (X,Y) . in my work the initial configurations were minimized at first then system equilibrated for 100 ps and followed by 500 ps production run. when I look at the .xtc and .gro file by vmd in the end of my work (after final mdrun), the particles are so much far from the sheet and realy no adsorption occur.sheet repulsed particles I also understood that after equilibration step the particle start to geting distance from sheet. I made the parameters of force field for the sheet by own ( bonding and nonbonding ) , because a proper force field for my compound didn't exist in defualt gromacs. why adsorption don't occur ? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Repulsion instead of adsorption
mina Madah wrote: Dear all I'm working on simulation of adsorption on the sheet . I use periodic boundary conditions in two dimension (X,Y) . in my work the initial configurations were minimized at first then system equilibrated for 100 ps and followed by 500 ps production run. when I look at the .xtc and .gro file by vmd in the end of my work (after final mdrun), the particles are so much far from the sheet and realy no adsorption occur.sheet repulsed particles I also understood that after equilibration step the particle start to geting distance from sheet. I made the parameters of force field for the sheet by own ( bonding and nonbonding ) , because a proper force field for my compound didn't exist in defualt gromacs. why adsorption don't occur ? Either your model (parameters, initial configuration, etc) is wrong or you didn't simulate long enough. 500 ps is an extremely short timeframe. -Justin any help will highly appreciated. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation using Martini force field
On 15/02/11 06:34, XAvier Periole wrote: You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of coil for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini coil is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! Agree with Xavier. I am working exactly on a coarse grained generic FF that could allow this kind of simulations, but it's far from being production ready -not an easy task at all. :) thanks for your support devicerandom! Uh... was it sarcastic or are you serious? (in any case: welcome!) XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- http://devicerandom.org -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] on force fields
Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Thanks. Your help is greatly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf reference structure?
Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? Thanking in advance for clarification. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] on force fields
On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file. 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf reference structure?
On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote: Dear all, I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms with reference to the average structure between 5-10 ns of a total of 10 ns simulation as below; g_rmsf ?f md.xtc ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg My understanding of the RMSF is as follows; RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2) where T is the time over which one wants to average, and Xi is the reference position of particle i, which is the time-averaged position of the same particle i. What I am confused is whether g_rmsf takes the reference structure from the structure file (-s), which in my case, the md.tpr and NOT the time averaged position over the specified time? It does take the reference structure from -s. Whether you actually want the RMSF from the non-physical time-averaged structure is up to you. IIRC you might be able to get such an average from g_cluster. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Conatant pH simulation in GROMACS
Hi all, I want to know that, whether we I can do constant pH simulation in gromacs. Please provide some details regarding this. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Conatant pH simulation in GROMACS
On 16/02/2011 6:04 PM, bipin singh wrote: Hi all, I want to know that, whether we I can do constant pH simulation in gromacs. Please provide some details regarding this. Please search first ;-) http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
