Re: [gmx-users] Genion error
On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- Depending on your Gromacs version, this command may not be right. Ion names were changed as of version 4.5. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Genion error
Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. Regards, Andrés F. *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia 2013/10/24 Justin Lemkul jalem...@vt.edu On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- Depending on your Gromacs version, this command may not be right. Ion names were changed as of version 4.5. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Genion error
On 10/24/13 10:21 AM, felipe vasquez wrote: Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. You don't want to embed ions into your protein or haphazardly into the system. You'll start deleting random segments of molecules, or the command will simply fail. You need to be replacing solvent molecules (usually water). Please consult some basic tutorial material; such selections are always covered. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] genion doesn't recognize SOL in top file
On 10/17/13 1:01 PM, sunyeping wrote: Dear Gromacs users, I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np 8 but it returns a error message saying: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' I checked the topol.top file, but SOL is indeed under [ molecules ] section: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 DRG 1 SOL 86574 I know it problem has been disscussed here before, but I cann't fix it out with the avialable information. Could you help me with it? You probably have a non-Unix newline character somewhere. Run the .top file through dos2unix and try again. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Genion command not working
Hi Deepak, You have to set the minimal distance between ions lower. Check the help of genion. Cheers, Tsjerk On Aug 28, 2013 8:04 AM, Deepak Ojha alwaysinthem...@gmail.com wrote: Dear Gmxers, I want to simulate 5M nabr aqueous solution.To add the ions I use genion command and add 22 na and br ions respectively to the system of pure 108 water molecules.But on running the command genion I get error message Processing topology Back Off! I just backed up topol.top to ./#topol.top.9# Replacing solvent molecule 12 (atom 36) with NA Replacing solvent molecule 52 (atom 156) with CL Replacing solvent molecule 35 (atom 105) with NA Replacing solvent molecule 17 (atom 51) with CL Replacing solvent molecule 41 (atom 123) with NA Replacing solvent molecule 70 (atom 210) with CL Replacing solvent molecule 44 (atom 132) with NA Replacing solvent molecule 66 (atom 198) with CL Replacing solvent molecule 34 (atom 102) with NA Replacing solvent molecule 29 (atom 87) with CL --- Program genion, VERSION 4.0.7 Source code file: ../../../../src/tools/gmx_genion.c, line: 85 Fatal error: No more replaceable solvent! --- How should I add ions in the system.I have tried doing it but could not get it please if someone may point my error. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live -- 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] genion
On 5/3/13 11:27 AM, Ewaru wrote: Hi, Just wondering. My system shows this: System has non-zero total charge: 11.98 and thus, I use the command as below to add 12 Cl to the protein: genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn 12 However, when I checked the genion.log file, it shows that the system has total charge of 12. Isn't it supposed to be 0? This is what the genion.log shows: The charge that genion reports is the one that it finds in the system contained in the .tpr file. grompp reports a net charge of 12 (or close enough to it, see http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) and genion confirms that is what it finds. The next invocation of grompp will confirm that your net charge is zero. -Justin Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Using shifted Lennard-Jones, switch between 0 and 1 nm Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 12.000 Generated table with 1200 data points for Ewald. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Shift. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC-like water optimization for 3745014 molecules. Thank you. Best regards, -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Justin A. Lemkul, Ph.D. Research Scientist 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] Genion cannot read from input
On 4/27/13 11:21 AM, Nathan Bullock wrote: I am running genion neutralize the charge of my protein. I got an error that wasn't very descriptive Fatal error: Cannot read from input The part of the script that called this program read as follows /usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c filled_box.pdb -p protein_mod_filled5.top -o ions.tpr Was ions.tpr successfully generated? /usr/local/gromacs-4.5.5/bin/genion -s ions.tpr -o solv_ions.pdb -p protein_mod_filled5.top -pname NA -nname CL -nn 3 I am using the amber03 force field. I had read on some of the pages that different forcefields used different nomenclature for the ions used to neutralize the charge. This is no longer true as of Gromacs 4.5, which has standardized nomenclature. You can always check ions.itp for your force field to be sure. The cannot read from input error only arises if (1) you are specifying a nonexistent index group (not applicable here) or (2) presumably if some input file does not exist. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Genion cannot read from input
On 4/27/13 12:28 PM, Justin Lemkul wrote: On 4/27/13 11:21 AM, Nathan Bullock wrote: I am running genion neutralize the charge of my protein. I got an error that wasn't very descriptive Fatal error: Cannot read from input The part of the script that called this program read as follows /usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c filled_box.pdb -p protein_mod_filled5.top -o ions.tpr Was ions.tpr successfully generated? /usr/local/gromacs-4.5.5/bin/genion -s ions.tpr -o solv_ions.pdb -p protein_mod_filled5.top -pname NA -nname CL -nn 3 I am using the amber03 force field. I had read on some of the pages that different forcefields used different nomenclature for the ions used to neutralize the charge. This is no longer true as of Gromacs 4.5, which has standardized nomenclature. You can always check ions.itp for your force field to be sure. The cannot read from input error only arises if (1) you are specifying a nonexistent index group (not applicable here) or (2) presumably if some input file does not exist. Edit: the reason your script fails is that genion requires you to select a group for replacement. You don't provide one, so it doesn't know what to read. See the following: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] genion doesn't work in 4.6.1?
Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin On 2013-04-05, at 1:05 PM, Albert mailmd2...@gmail.com wrote: Hello: I found that there would be some problem of genion in 4.6.1: grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr NOTE 1 [file complex.top, line 44008]: System has non-zero total charge: -11.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. Obviously, the total charge of the system is -11.0, but genion doesn't add anything to netural it thank you very much best Albert -- 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] genion doesn't work in 4.6.1?
On Fri, Apr 5, 2013 at 3:05 PM, Albert mailmd2...@gmail.com wrote: Hello: I found that there would be some problem of genion in 4.6.1: grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr NOTE 1 [file complex.top, line 44008]: System has non-zero total charge: -11.00 Total charge should normally be an integer. See http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetichttp://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. Obviously, the total charge of the system is -11.0, but genion doesn't add anything to netural it thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] genion doesn't work in 4.6.1?
On Fri, Apr 5, 2013 at 3:05 PM, Albert mailmd2...@gmail.com wrote: Hello: I found that there would be some problem of genion in 4.6.1: grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr NOTE 1 [file complex.top, line 44008]: System has non-zero total charge: -11.00 Total charge should normally be an integer. See http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetichttp://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. Obviously, the total charge of the system is -11.0, but genion doesn't add anything to netural it genion has never done anything if you just use -neutral. You need to use -neutral in conjunction with -conc, otherwise manually specify the number of ions to add. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] genion doesn't work in 4.6.1?
On 04/05/2013 09:09 PM, Warren Gallin wrote: Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin No, it doesn't work either: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -nname CL or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -pq 11 Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. -- 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] genion doesn't work in 4.6.1?
On Fri, Apr 5, 2013 at 3:09 PM, Warren Gallin wgal...@ualberta.ca wrote: Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Default names are used (see genion -h), and the default names are correct for all force fields as of version 4.5, which standardized ion nomenclature across force fields. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] genion doesn't work in 4.6.1?
On 04/05/2013 09:09 PM, Warren Gallin wrote: Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin No, it doesn't work either: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -nname CL or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -pq 11 Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. You are using the wrong combinations of flags: Either of the following should do the job: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11 -pq 1 or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral (incase you want a NaCl conc of 0.15 M. Only in this case, genion will automatically add NA and CL ions to neutralize the charge and sufficiently reach the given conc., in this case 0.15 M) Cheers. Abhishek Acharya Structural and Computational Biology Lab Indian Institute of Technology Kanpur -- 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] genion doesn't work in 4.6.1?
Again and again posting from Abhishek Acharya or Shima, or Rama David or somehow else ... pls read my posting before, it could be useful for you, Indian fellows ... maybe it's possible to get some kind of agreement though brahmin.net or so .. Best regards of somebody experienced with Indian science Best, Felipe From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Abhishek Acharya [aacha...@iitk.ac.in] Sent: Friday, April 05, 2013 9:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genion doesn't work in 4.6.1? On 04/05/2013 09:09 PM, Warren Gallin wrote: Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin No, it doesn't work either: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -nname CL or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -pq 11 Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. You are using the wrong combinations of flags: Either of the following should do the job: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11 -pq 1 or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral (incase you want a NaCl conc of 0.15 M. Only in this case, genion will automatically add NA and CL ions to neutralize the charge and sufficiently reach the given conc., in this case 0.15 M) Cheers. Abhishek Acharya Structural and Computational Biology Lab Indian Institute of Technology Kanpur -- 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] genion doesn't work in 4.6.1?
Again and again posting from Abhishek Acharya or Shima, or Rama David or somehow else ... pls read my posting before, it could be useful for you, Indian fellows ... maybe it's possible to get some kind of agreement though brahmin.net or so .. Best regards of somebody experienced with Indian science Best, Felipe Dear Luis I hope you do realize that this is a open for all forum to discuss and sort out problems. And also that posting such prejudiced comments are not in the right spirit for this or any other forum related to science. But since you have posted I would take the opportunity for once to point out that if there were any shortage of supervision, there would be about a 1000 queries alone from Indians each day. So the take home message is that only people who don't have anyone in the vicinity to solve their problems and are stuck, post questions on this forum, and this is not in any way a function of the geographical region or race a person belongs. Can happen to anyone. I hope in the future you don't bring your personal prejudices, whatever may be your experience with Indian science, into this forum. With Regards Abhishek Acharya From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Abhishek Acharya [aacha...@iitk.ac.in] Sent: Friday, April 05, 2013 9:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genion doesn't work in 4.6.1? On 04/05/2013 09:09 PM, Warren Gallin wrote: Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin No, it doesn't work either: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -nname CL or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -pname NA -pq 11 Reading file ions.tpr, VERSION 4.6.1 (single precision) Using a coulomb cut-off of 1.2 nm No ions to add and no potential to calculate. You are using the wrong combinations of flags: Either of the following should do the job: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11 -pq 1 or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral (incase you want a NaCl conc of 0.15 M. Only in this case, genion will automatically add NA and CL ions to neutralize the charge and sufficiently reach the given conc., in this case 0.15 M) Cheers. Abhishek Acharya Structural and Computational Biology Lab Indian Institute of Technology Kanpur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genion problem with divalent ions
On 9/9/12 7:53 AM, Matthias Ernst wrote: Hi, I just encountered (another) strange thing with genion. I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2, forcefield amber99sb), so I expected half of the system charge (-52) to be added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26 which would be needed for neutralization. The same holds for Zn or Ca ions, which also are divalent in ions.itp Charge is not read from ions.itp, it is taken from the command line. The value of -pq is 1, so if you're adding divalent metals, set it to 2. Could it be that the routines of genion to determine the number of ions are not working properly? I mean, the -neutral option also does work only if the -conc flag is also there and provides a value 0.0 (which in fact is not what I want when I just want do neutralize my system by adding ions...) This has been an issue for a long time. I suppose no one has ever filed a redmine issue for it, so please do. Otherwise, it won't get fixed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] genion problem with divalent ions
Hi there, In addition to setting -pq to 2 as Justin said, you can set -conc to a very low value such as 0.1 for neutralizing the system. One more thing... genion apparently uses the box volume when determining how many ions are necessary for getting a given ionic strength. However, depending of your system size and shape and box type the volume of the protein may be considerable. Maybe the number of water molecules, instead of the box volume, is a better criterion for determining the number of ions to be added. best regards, Leandro 2012/9/9 Matthias Ernst un...@student.kit.edu Hi, I just encountered (another) strange thing with genion. I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2, forcefield amber99sb), so I expected half of the system charge (-52) to be added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26 which would be needed for neutralization. The same holds for Zn or Ca ions, which also are divalent in ions.itp Could it be that the routines of genion to determine the number of ions are not working properly? I mean, the -neutral option also does work only if the -conc flag is also there and provides a value 0.0 (which in fact is not what I want when I just want do neutralize my system by adding ions...) Does anyone of you also had similar problems? Thank you, Matthias -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] genion
Eduardo Oliveira wrote: Hi all, I' ve stumbled upon a problem when i used genion to prepare my files. Here's the comand line: genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq -1 -p sistema.toI I've got this in return: Fatal error: Your solvent group size (73282) is not a multiple of 19. What did you choose as the group in which to insert ions? If you chose System, that's an incorrect approach. I would suggest you refer to to some basic tutorial material to make these workflows more clear. http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use -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/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] genion
Eduardo Oliveira wrote: First, thanks for the help! Yeah i chose System. But, regardless my wrong choice, I still want to know why does the solvent group need to be a multiple pf 19 or whatever number for that matter. I searched in the gmx-users mailling list and noticed that this is a common occurance. What genion does is replace a continuous group of solvent molecules with ions. In order to do that, it needs to know how many atoms are in each solvent molecule. In the case of water, the OW atom is replaced by the ion and the following 2 H atoms are deleted, because genion detects that water has 3 atoms. In your case, whatever the first molecule in your system is has 19 atoms, and thus genion assumes that the remaining molecules in the group System are each composed of 19 atoms. When it finds that this is not the case, it triggers a fatal error, rather than merrily deleting 19 atoms at a time to give a horribly fragmented, completely useless system. -Justin *De:* Justin A. Lemkul jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Sábado, 31 de Março de 2012 14:25 *Assunto:* Re: [gmx-users] genion Eduardo Oliveira wrote: Hi all, I' ve stumbled upon a problem when i used genion to prepare my files. Here's the comand line: genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq -1 -p sistema.toI I've got this in return: Fatal error: Your solvent group size (73282) is not a multiple of 19. What did you choose as the group in which to insert ions? If you chose System, that's an incorrect approach. I would suggest you refer to to some basic tutorial material to make these workflows more clear. http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use -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 -- 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] genion -pname no NA molecule (sodium) type
On 17/03/2012 4:57 PM, Wholly Peach wrote: Will you please tell me where can I find the ions.itp file? http://www.gromacs.org/Documentation/Terminology/Environment_Variables 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] genion -pname no NA molecule (sodium) type
On 17/03/2012 4:48 PM, Wholly Peach wrote: Dear All, I use the following to neutralize the charge genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8, Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr. However the feedback says there is no Na (sodium) moleculetype. Your force field defines [moleculetype] sections for ions in its ions.itp file. Go and look at it, compare with your .top and see what the problem is. Atom names, residue names and moleculetype names are all different things, and each part of your .top must match the right name at the right time. 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] genion -pname no NA molecule (sodium) type
Will you please tell me where can I find the ions.itp file? I am looking forward to getting your reply. Wholly From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, 17 March 2012 3:55 PM Subject: Re: [gmx-users] genion -pname no NA molecule (sodium) type On 17/03/2012 4:48 PM, Wholly Peach wrote: Dear All, I use the following to neutralize the charge genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8, Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr. However the feedback says there is no Na (sodium) moleculetype. Your force field defines [moleculetype] sections for ions in its ions.itp file. Go and look at it, compare with your .top and see what the problem is. Atom names, residue names and moleculetype names are all different things, and each part of your .top must match the right name at the right time. Mark -- 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] genion doubt
HI I'm not sure about this kind of error but as per my knowledge the problem might be with the parameter cpp in mdp file. In my mdp file it is as follows title = ecoli_nusG cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 10 ; total 100 ps. nstcomm = 1 .. .. and somewhere i read the nsteps should be between 5-10 for pr dynamics. search gromacs tutorial for better clue... [?] On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan manju...@gmail.comwrote: hi snip Thank u. as per ur suggestion i added sodium ions to my protein. then i carried out mdrun for energy minimization nsteps 3000 but i runs only for 1108 steps. then i went to position restrain steps the command i gave grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr i got a fatal error Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option WARNING 1 [file pr.mdp, line unknown]: Unknown or double left-hand 'warnings' in parameter file y i'm getting this error.how can i correct this could any one help plz. my pr.mdp file title = FWS warnings= 10 cpp = /usr/local/gromacs/share/gromacs/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500 ; total 1.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 with this warnings i proceeded with mdrun but i get the following LINCS warnnings starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 300, will finish Sat May 15 08:57:23 2010 Step 394, time 0.788 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000103, max 0.001028 (between atoms 4478 and 4480) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4478 4480 33.40.1081 0.1091 0.1090 Step 423, time 0.846 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.442275, max 40.666431 (between atoms 8211 and 8212) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 8473 8476 88.60.1527 0.2741 0.1522 8473 8475 89.90.1094 3.6185 0.1090 8473 8474 89.50.1094 0.2778 0.1090 8471 8473 87.20.1455 0.2548 0.1449 8471 8472 33.20.1013 0.1241 0.1010 8215 8217 32.80.1090 0.1240 0.1090 8215 8216 39.20.1091 0.1282 0.1090 8211 8215 45.80.1536 0.1603 0.1529 8211 8213 44.00.1425 0.1645 0.1410 8211 8212 90.20.4225 4.5416 0.1090 8209 8211 45.60.1511 0.1348 0.1529 8209 8210 32.40.1098 0.1199 0.1090 8207 8209 33.30.1482 0.1823 0.1449 7224 7225 30.40.1013 0.1010 0.1010 5296 5297 30.50.1093 0.1092 0.1090 Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 424, time 0.848 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 171806.092017, max 19412182.00 (between atoms 8235 and 8236) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 8507 8508 90.00.1011 0.2179 0.1010 8497 8499 39.80.1460 0.2065 0.1449 8497 8498 59.80.1009 0.1923 0.1010 8495 8497 44.00.1354 729.7847 0.1335 8495 8496 94.40.1235 729.7617 0.1229 8491 8493 89.70.1091 0.2077 0.1090 8487 8489
Re: [gmx-users] genion doubt
manjula kasinathan wrote: hi snip Thank u. as per ur suggestion i added sodium ions to my protein. then i carried out mdrun for energy minimization nsteps 3000 but i runs only for 1108 steps. then i went to position restrain steps the command i gave grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr i got a fatal error Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option WARNING 1 [file pr.mdp, line unknown]: Unknown or double left-hand 'warnings' in parameter file y i'm getting this error.how can i correct this could any one help plz. http://www.gromacs.org/Documentation/Errors#Unknown_left-hand__in_parameter_file Read the manual - there is no such setting as warnings. my pr.mdp file title = FWS warnings= 10 cpp = /usr/local/gromacs/share/gromacs/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500 ; total 1.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 with this warnings i proceeded with mdrun but i get the following LINCS warnnings starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 300, will finish Sat May 15 08:57:23 2010 Step 394, time 0.788 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000103, max 0.001028 (between atoms 4478 and 4480) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4478 4480 33.40.1081 0.1091 0.1090 Step 423, time 0.846 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.442275, max 40.666431 (between atoms 8211 and 8212) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 8473 8476 88.60.1527 0.2741 0.1522 8473 8475 89.90.1094 3.6185 0.1090 8473 8474 89.50.1094 0.2778 0.1090 8471 8473 87.20.1455 0.2548 0.1449 8471 8472 33.20.1013 0.1241 0.1010 8215 8217 32.80.1090 0.1240 0.1090 8215 8216 39.20.1091 0.1282 0.1090 8211 8215 45.80.1536 0.1603 0.1529 8211 8213 44.00.1425 0.1645 0.1410 8211 8212 90.20.4225 4.5416 0.1090 8209 8211 45.60.1511 0.1348 0.1529 8209 8210 32.40.1098 0.1199 0.1090 8207 8209 33.30.1482 0.1823 0.1449 7224 7225 30.40.1013 0.1010 0.1010 5296 5297 30.50.1093 0.1092 0.1090 Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 424, time 0.848 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 171806.092017, max 19412182.00 (between atoms 8235 and 8236) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 8507 8508 90.00.1011 0.2179 0.1010 8497 8499 39.80.1460 0.2065 0.1449 8497 8498 59.80.1009 0.1923 0.1010 8495 8497 44.00.1354 729.7847 0.1335 8495 8496 94.40.1235 729.7617 0.1229 8491 8493 89.70.1091 0.2077 0.1090 8487 8489 89.80.1091 0.5344 0.1090 8485 8491 32.70.1531 0.1890 0.1529 8485 8486 47.40.1091 0.1421 0.1090 8482 8485 50.70.1536 215.0330 0.1529 8482 8484 71.00.1094 214.9777 0.1090 8482 8483 92.60.1091 215.0566 0.1090 8480 8495 77.10.1633 417.3555 0.1522 8480 8482 84.20.1556 871.1644 0.1529 8480 8481 80.70.1078 911.5953
Re: [gmx-users] genion doubt
Bharath.K. Chakravarthi wrote: HI I'm not sure about this kind of error but as per my knowledge the problem might be with the parameter cpp in mdp file. In my mdp file it is as follows The problem is unrelated to cpp, since the error complained about the use of warnings in the .mdp file. Further, if we are to assume Gromacs 4.0.x, the cpp setting is ignored, as Gromacs has its own C pre-processor now. title = ecoli_nusG cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 10 ; total 100 ps. nstcomm = 1 .. .. and somewhere i read the nsteps should be between 5-10 for pr dynamics. In general, yes, to obtain good equilibration you would certainly want to run for more than 1.0 ps, but I would say there is no absolute setting that should be applied. -Justin search gromacs tutorial for better clue... On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan manju...@gmail.com mailto:manju...@gmail.com wrote: hi snip Thank u. as per ur suggestion i added sodium ions to my protein. then i carried out mdrun for energy minimization nsteps 3000 but i runs only for 1108 steps. then i went to position restrain steps the command i gave grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr i got a fatal error Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option WARNING 1 [file pr.mdp, line unknown]: Unknown or double left-hand 'warnings' in parameter file y i'm getting this error.how can i correct this could any one help plz. my pr.mdp file title = FWS warnings= 10 cpp = /usr/local/gromacs/share/gromacs/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500 ; total 1.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 with this warnings i proceeded with mdrun but i get the following LINCS warnnings starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 300, will finish Sat May 15 08:57:23 2010 Step 394, time 0.788 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000103, max 0.001028 (between atoms 4478 and 4480) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4478 4480 33.40.1081 0.1091 0.1090 Step 423, time 0.846 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.442275, max 40.666431 (between atoms 8211 and 8212) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 8473 8476 88.60.1527 0.2741 0.1522 8473 8475 89.90.1094 3.6185 0.1090 8473 8474 89.50.1094 0.2778 0.1090 8471 8473 87.20.1455 0.2548 0.1449 8471 8472 33.20.1013 0.1241 0.1010 8215 8217 32.80.1090 0.1240 0.1090 8215 8216 39.20.1091 0.1282 0.1090 8211 8215 45.80.1536 0.1603 0.1529 8211 8213 44.00.1425 0.1645 0.1410 8211 8212 90.20.4225 4.5416 0.1090 8209 8211 45.60.1511 0.1348 0.1529 8209 8210 32.40.1098 0.1199 0.1090 8207 8209 33.30.1482 0.1823 0.1449 7224 7225 30.40.1013 0.1010 0.1010 5296 5297 30.50.1093 0.1092 0.1090 Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation
Re: [gmx-users] genion: can you place the ions at one location in the box?
Justin A. Lemkul wrote: Smiruthi Ramasubramanian wrote: Justin, I tried to use an index file with atom numbers of the water molecules in the required volume. But when I try to ionize the box, I get this error: Fatal error: The solvent group SOL is not continuous: index[717]=21689, index[718]=21696 This makes sense, but is there a way get around this? The fundamental requirement of genion is that the solvent is continuous in the coordinate file. If that's not true, genion won't work. If you have continuous solvent, a valid index group within that section should work just fine. Another option is to write your own script that replaces water molecules with the desired ion type; it should be relatively simple to randomly choose water molecules to replace based on simple coordinate criteria. Updating the topology would have to be done manually, and you'd have to find a way to generate a syntactically correct coordinate file after making replacements, but that is also fairly simple I/O with, for example, Perl. -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] genion: can you place the ions at one location in the box?
Smiruthi Ramasubramanian wrote: I am simulating an ion channel and require help placing a concentration of ions at one side of the box (below the membrane). Sidedness is irrelevant in a periodic system; the water layers are continuous with PBC. SETUP: membrane + embedded protein in the center of the cube. I tried to generate a smaller cube (of the required volume below the cube), solvate, add ions and then /cat/ with the *.gro file of my system before solvating. But when I solvate the system with ions, the ions are removed. Any suggestions as to how to handle this problem? I don't fully understand what you tried to do, but it should be possible to solvate the unit cell normally, create an index group for the waters on one side of the membrane, and pass this index file to the -n flag of genion. Creating the index file may involve writing your own script to collect the atom numbers. As far as I am aware, make_ndx cannot, for example, select all water molecules below/above some z-coordinate, which would be required for your situation. -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] genion
leila karami wrote: Hi total charge of my system (pr-dna) is (-10). which is better in genion command: 1) 10 Na or 2) 20 NA + 10 Cl http://www.gromacs.org/Documentation/Gromacs_Utilities/genion Additional ions model increased ionic strength. Whether or not that is better is up to you based on the desired model. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] genion question
Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? Payman On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: I realized sth about the previous error message I posted. In the following I have copied the lines (with their line number) which grompp gives warning on! in .gro file: 65868 10940SOLHW265866 5.038 5.739 6.407 65869 10940SOL MW65867 5.103 5.710 6.455 65870 10940SOLLP165868 5.061 5.644 6.524 65871 10940SOLLP265869 5.144 5.630 6.405 65872 10941Na Na65870 1.844 0.957 1.889 658735.4 6.23500 10.24600 in .top file: 4147 [ molecules ] 4148 ; Compound#mols 4149 Protein_A 1 4150 SOL 10903 4151 Na+ 1 I have tested that if I remove the + sign, grompp will not work at all and says such molecule does not exists. So, I am not sure where the Na-NA mismatch comes from?! Ion names are force field-specific. If you left -pname as the default, it assigns Na (for ffgmx). Check ions.itp for the correct name. -Justin Payman On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: When I look at the .top file generated by pdb2gmx, the last lines show how this -0.99 is generated: 442 opls_302 37ARG CZ138 0.64 12.011 ; qtot -0.33 443 opls_300 37ARGNH1139 -0.814.0067 ; qtot -1.13 444 opls_301 37ARG HH11139 0.46 1.008 ; qtot -0.67 445 opls_301 37ARG HH12139 0.46 1.008 ; qtot -0.21 446 opls_300 37ARGNH2140 -0.814.0067 ; qtot -1.01 447 opls_301 37ARG HH21140 0.46 1.008 ; qtot -0.55 448 opls_301 37ARG HH22140 0.46 1.008 ; qtot -0.09 449 opls_271 37ARG C1410.7 12.011 ; qtot 0.61 450 opls_272 37ARG O1141 -0.815.9994 ; qtot -0.19 451 opls_272 37ARG O2141 -0.815.9994 ; qtot -0.99 The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of simulation is supposed to be close to 7.0, I believe one of the negatively-charged side chains needs to be neutralized. That's why I think one Na+ might be helpful. That's probably correct. I just wanted to verify what was in your system. If you just had water, it made no sense. But with a protein involved with lots of partial charges, these rounding issues do occur. You really do have a system with -1 charge. -Justin Payman On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: OK! It worked! Thanks a lot again. But I have a final technical question. After running grompp, it shows that my box has a net charge of -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is OK?! or even this 0.01 charge will cause me troubles? Depending on the size of your system, rounding errors can occur. It is unusual that the hundredths place would be showing this error. Usually you'd get something like 0.8 or something. Your water topology has a zero net charge; is there something else in your system causing the -1 charge? Adding a single Na+ to neutralize the charge may be appropriate, but that's up to you based on what's in your system (something else may be broken, but I just don't know). -Justin Sorry for tons of e-mails. regards, Payman On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: OK! That's fine. But what if I do not have permissions to make such changes in the itp files? Also, isn't that the case that when you define That's why I said copy the force field files into your local directory. Once there, you can modify them. sth for the second time, grompp will take the second one? Sorry for mass of e-mail! That is only true in the case of .mdp files. -Justin Payman On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: I have done that already! I use my local copy to make my files. but how can I get rid of this error? get into the oplsaanb.itp or include this water model in the topology file before oplsaa.itp? I don't understand what you're saying you've already done. The problem is this: when grompp attempts to assemble the .tpr file, it reads all of the information from the ffoplsaa*.itp files. It finds the directives like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a duplicate of these directives, it complains. So when you #include your .itp file
Re: [gmx-users] genion question
Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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] genion question
Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] genion question
Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong! Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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] genion question
Well, if I have understood your words properly, apparently there is a problem in the first residue in amino terminal which I treated the NH2 as a zwitterionic piece(+1), and gave the side chain -1 charge. I thought it should add up to zero, but apparently it does not: 1 opls_287 1ASP N 1 -0.314.0067 ; qtot -0.3 2 opls_290 1ASP H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1ASP H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1ASP H3 1 0.33 1.008 ; qtot 0.69 5 opls_299 1ASP CA 1 0.15 12.011 ; qtot 0.84 6 opls_140 1ASP HA 1 0.06 1.008 ; qtot 0.9 7 opls_274 1ASP CB 2 -0.22 12.011 ; qtot 0.68 8 opls_140 1ASPHB1 2 0.06 1.008 ; qtot 0.74 9 opls_140 1ASPHB2 2 0.06 1.008 ; qtot 0.8 10 opls_271 1ASP CG 30.7 12.011 ; qtot 1.5 11 opls_272 1ASPOD1 3 -0.815.9994 ; qtot 0.7 12 opls_272 1ASPOD2 3 -0.815.9994 ; qtot -0.1 13 opls_235 1ASP C 40.5 12.011 ; qtot 0.4 14 opls_236 1ASP O 4 -0.515.9994 ; qtot -0.1 What do you think? Payman On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong! The total charge will undoubtedly fluctuate. What's most important to look at is when you reach the end of a residue and you do not see an integer charge. -Justin Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Paymon Pirzadeh wrote: Well, if I have understood your words properly, apparently there is a problem in the first residue in amino terminal which I treated the NH2 as a zwitterionic piece(+1), and gave the side chain -1 charge. I thought it should add up to zero, but apparently it does not: You chose the wrong terminus. The Zwitterion-NH3+ species is for an isolated amino acid containing both NH3+ and COO- alpha-carbon substituents. Choose a plain NH3+ for your terminus. -Justin 1 opls_287 1ASP N 1 -0.314.0067 ; qtot -0.3 2 opls_290 1ASP H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1ASP H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1ASP H3 1 0.33 1.008 ; qtot 0.69 5 opls_299 1ASP CA 1 0.15 12.011 ; qtot 0.84 6 opls_140 1ASP HA 1 0.06 1.008 ; qtot 0.9 7 opls_274 1ASP CB 2 -0.22 12.011 ; qtot 0.68 8 opls_140 1ASPHB1 2 0.06 1.008 ; qtot 0.74 9 opls_140 1ASPHB2 2 0.06 1.008 ; qtot 0.8 10 opls_271 1ASP CG 30.7 12.011 ; qtot 1.5 11 opls_272 1ASPOD1 3 -0.815.9994 ; qtot 0.7 12 opls_272 1ASPOD2 3 -0.815.9994 ; qtot -0.1 13 opls_235 1ASP C 40.5 12.011 ; qtot 0.4 14 opls_236 1ASP O 4 -0.515.9994 ; qtot -0.1 What do you think? Payman On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong! The total charge will undoubtedly fluctuate. What's most important to look at is when you reach the end of a residue and you do not see an integer charge. -Justin Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
Re: [gmx-users] genion command with PDB files for amber03 force field
Hi, To set things straight a bit. If you are using ion-related GROMACS tools, such as genion, you will need to enter the AMBER ion definition to the ions.itp file in the top directory of the GROMACS distribution. This isn't too tough, as all the parameters for the ions are included with the Amber ports, but genion needs them to be in the ions.itp (or other suitable) file. This has nothing to do with genion. Genion just uses the names for ions that are given (either explicitly or as default) with options -pname and -nname. When the ions occur in the system (under [ system ] in the .top file), they have to be defined somewhere as moleculetypes. Otherwise grompp will complain; no other program. ions.itp is just an intuitive place for these moleculetype definitions. Please inform yourself well regarding the way gromacs handles topologies. Check chapter 5 of the manual. This goes double when answering posts on such topics. Although such efforts are commonly appreciated, (partly) wrong information may send the original poster further off. Dear gromacs users, I am using genion command to add ions to .tpr file which was made for protein by use of amber03 force field. In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx. This is not a big problem , but it looks is a little bit like a bug. Justin answered this part of the question. For a suitable scheme to set up your simulations, you may want to check http://www.nmr.chem.uu.nl/~tsjerk/course/molmod/md.html Cheers, Tsjerk -- 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion command with PDB files for amber03 force field
Andrew, Just ran into this myself. If you read the notes on http://chemistry.csulb.edu/ffamber/#usage closely, you'll find this little tid-bit: If you are using ion-related GROMACS tools, such as genion, you will need to enter the AMBER ion definition to the ions.itp file in the top directory of the GROMACS distribution. This isn't too tough, as all the parameters for the ions are included with the Amber ports, but genion needs them to be in the ions.itp (or other suitable) file. Cheers, Josh On Mar 5, 2009, at 9:44 AM, drugdesign wrote: Dear gromacs users, I am using genion command to add ions to .tpr file which was made for protein by use of amber03 force field. In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx. This is not a big problem , but it looks is a little bit like a bug. Best regards, Andrew ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion command with PDB files for amber03 force field
drugdesign wrote: Dear gromacs users, I am using genion command to add ions to .tpr file which was made for protein by use of amber03 force field. In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx. PDB format dictates 3 characters for writing residue names. If you want to keep NHIE, use .gro format. What next pdb2gmx are you talking about? If you've written your topology (the first step), there should be no reason to run pdb2gmx again during system preparation. -Justin This is not a big problem , but it looks is a little bit like a bug. Best regards, Andrew ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genion failing in parallel runs.
Bhanu wrote: Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated: Program genion_d Version 3.3.3 sourcecode file: init.c, line 69 Fatal error: run input file prakash.tpr was made for 32 nodes while genion_d expected it to be for 1 node -- System is protein in water, dodecahedron box. Everything is fine till energy minimisation. genion is failing. Any clue?? The problem is that genion is not MPI code, i.e., not parallelized. Usually one does all of the preparation steps (pdb2gmx, editconf, genion) at one time, then begins MPI work - minimization, equilibration, production. -Justin Thanks. -- _ _ (_)(_) (,,) =()= ((__)\ _|L\___/ The Lab Rats When u r busy judging ppl, you've no time to love'em.. -Nick Vujicic ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genion failing in parallel runs.
Hi, On Tuesday, 26. August 2008, Bhanu wrote: Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated: Program genion_d Version 3.3.3 sourcecode file: init.c, line 69 Fatal error: run input file prakash.tpr was made for 32 nodes while genion_d expected it to be for 1 node --- use grompp without the '-np 32' option which defines the number of nodes. Genion runs on one node. After neutralization you have to run grompp again, than also with '-np 32' option. --- System is protein in water, dodecahedron box. Everything is fine till energy minimisation. genion is failing. Any clue?? Thanks. greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion
Hi sh-karbalaee, Well, running an MD simulation has nothing to do with genion per se. But it's better not to have a net chare in your system. Therefore you'd best add an ion (at the least) to your system with unit charge. Whether you do that using genion or do it by hand, is entirely up to you. Check the archives of the user list and the wiki... Counterions and charged systems have been discussed often. Cheers, Tsjerk On Thu, Jun 19, 2008 at 6:24 AM, shahrbanoo karbalaee [EMAIL PROTECTED] wrote: Dear justin thanks for reply about g_dist. about genion for peptides.Do I must use command genion for MD peptides with one charge(13 aa)?Is it necessary for md? best sh-karbalaee ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion problem: is replacing 84 water molecules instead of 200
Subhrangshu Supakar wrote: Hi All !! I have defined my own system which contains 200 water molecules, which I can see in the .gro file. Then I created the .tpr file for 200 steps to steep. In the confout file I can again see the 200 water molecules. But When I am trying to replace the 200 water molecules with 200 Na+ GROMACS is complaining: genion -h is your friend. check the -rmin option. Replacing solvent molecule 144 (atom 4632) with Na Replacing solvent molecule 193 (atom 4779) with Na Replacing solvent molecule 49 (atom 4347) with Na Replacing solvent molecule 84 (atom 4452) with Na --- Program genion, VERSION 3.3.2 Source code file: gmx_genion.c, line: 84 Fatal error: No more replaceable solvent! --- It is replacing 84 water molecules only (I used genion for this) Can any body help me? Thanx in advance. Subhrangshu Supakar ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genion: specify minimum distance between counter-ion and solute
Narayanan Veeraraghavan wrote: Hi, I was wondering if there was a way to specify a minimum distance between the counter-ion and solute, using Genion. There is a rmin option, buts thats for the dist between the ions. But, I am interested in the distance between ions and solute. Would appreciate any help. No there's no way to do that. I don't see much point in it anyway... opposite-charge ions will move inside that radius during the simulation anyway. Mark ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genion - hangs up
Hi Tsjerk Thanks for the mail. I think my machine got the problematic Gromacs version when it underwent a big upgrade since I never manually compiled Gromacs on it. In other words it looks like it got a problematic rpm(/deb etc) via Synaptic(/whatever). Is that possible - can this problem have fed through somewhere into prebuilt rpms/debs? I have managed to rectify the problem by using two rpms off the Gromacs website to first downgrade then upgrade again alien --scripts -i gromacs-3.2.1-1.i386.rpm alien --scripts -i gromacs-3.3-1.i386.rpm There were a couple of small errors/warnings but the system seems functional. Synaptic on another machine is suggesting an upgrade from 3.3-1 to 3.3.1-1. Is that safe to do? Thanks again for the help Luciane Dr Luciane Vieira de Mello School of Biological Sciences Room 2.20, Life Science Building Tel:(+44) 151 795 5140 FAX:(+44) 151 794 5130 University of Liverpool Crown St.,Liverpool L69 7ZB, U.K. -Original Message- From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar Sent: Thu 7/19/2007 7:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genion - hangs up Hi Luciane, David van der Spoel has replied saying: there is a problem compiling gromacs using gcc 4.x that may cause this. see a recent bugzilla entry about it. Did you compile using the 4.x gcc? In that case, recompile with an older version (3.x). That solution was suggested in the same discussion. While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so went to /tutor/speptide, but it was the same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine under 3.2. I've had this problem, but only with very high salinity. My solution to that problem (decreasing the allowed minimal distance between ions) is likely not going to work for you.v So I'd try recompiling if indeed you used the 4.x gcc version. I am wondering if this problem has already been fixed for version 3.3.1 and if a update for that is available. Is the only solution go back to 3.2? Frankly, we'd say the problem is with gcc, not with gromacs :) The gcc team should really fix what they've broken in the 4.x series :p Cheers, Tsjerk -- 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion - hangs up
Hi Luciane, David van der Spoel has replied saying: there is a problem compiling gromacs using gcc 4.x that may cause this. see a recent bugzilla entry about it. Did you compile using the 4.x gcc? In that case, recompile with an older version (3.x). That solution was suggested in the same discussion. While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so went to /tutor/speptide, but it was the same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine under 3.2. I've had this problem, but only with very high salinity. My solution to that problem (decreasing the allowed minimal distance between ions) is likely not going to work for you.v So I'd try recompiling if indeed you used the 4.x gcc version. I am wondering if this problem has already been fixed for version 3.3.1 and if a update for that is available. Is the only solution go back to 3.2? Frankly, we'd say the problem is with gcc, not with gromacs :) The gcc team should really fix what they've broken in the 4.x series :p Cheers, Tsjerk -- 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://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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion
Elias santos wrote: Hi!! I want know because we must neutralize the total load of the system (protein + water) into of the box with genion. You should neutralize the system and you also may want to add extra ions to get up to physiological salt concentration. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion - why shall we neutralize the charges?
Hi, First, our simulation system in physical world are mostly neutralized instead of carrying charges. Second, there is requirement for PME for electrostatic calculations. Neutralization is a not a must in 3.3.1 Gromacs; a background charge will complement for the charges that system carries, but it is always good to put explicit ions. Besides neutralization of charge, it is also reminded to keep total charge at an integer or very close to an integer (due to floating number representation in computer). A personal note to you: please use regular and scientific words for this mailing list. It is not easy to get to know what you are asking. Regards, Yang Ye - Original Message From: Elias santos [EMAIL PROTECTED] To: gmx-users gmx-users@gromacs.org Sent: Tuesday, June 12, 2007 1:34:39 AM Subject: [gmx-users] genion Hi!! I want know because we must neutralize the total load of the system (protein + water) into of the box with genion. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genion
What actually is it that you want to know about? Your email doesn't really specify anything that you are trying to find out. Are you wanting to maybe be able to neutralise the change in a system using genion? Have you looked at the tutorials and checked genion -h? -Original Message- From: [EMAIL PROTECTED] on behalf of Elias santos Sent: Sun 6/10/2007 4:21 AM To: gmx-users@gromacs.org Subject: [gmx-users] genion Hi!! I want know because we must neutralize the total load of the system (protein + water) in the interior of the box with genion. Elias winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion halted
Hi, the same one, gcc-4.1. Have you tried with other versions? Sampo andrea spitaleri wrote: Hi which gcc have you used for compiling gromacs? I have the same problem in one pc in which I have build gromacs using gcc-4.1 Regards andrea Sampo Karkola wrote: Dear list, the genion program gets halted when I'm trying to replace the solvent molecules with ions. The command genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top -pname NA+ -nname CL- -random -neutral -conc 0.1 asks for the group of solvent molecules and when I tell him to use it I get this output Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 9918 Processing topology Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ and 21 CL- ions. Back Off! I just backed up fdt.top to ./#fdt.top.2# Replacing solvent molecule 1163 (atom 6250) with NA+ and then nothing happens. genion.log gets generated only half way. My system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via synaptic and also built from source. The same thing happens in both of them. Gromacs version is 3.3.1. However, when I try the same thing on another machine, a HP Proliant ML350 with Debian Sarge and Gromacs 3.3.1, everything goes well. None of the gromacs programs gives any errors before genion. I'll give you more info about the system configuration if anyone asks :) Sampo ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion halted
Hi, so you got genion working with 4.0.2? Sampo andrea spitaleri wrote: gcc-4.0.2 seems ok for gmx-3.3.1 I have also submitted in bugzilla a similar problem with g_rdf Regards andrea Sampo Karkola wrote: Hi, the same one, gcc-4.1. Have you tried with other versions? Sampo andrea spitaleri wrote: Hi which gcc have you used for compiling gromacs? I have the same problem in one pc in which I have build gromacs using gcc-4.1 Regards andrea Sampo Karkola wrote: Dear list, the genion program gets halted when I'm trying to replace the solvent molecules with ions. The command genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top -pname NA+ -nname CL- -random -neutral -conc 0.1 asks for the group of solvent molecules and when I tell him to use it I get this output Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 9918 Processing topology Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ and 21 CL- ions. Back Off! I just backed up fdt.top to ./#fdt.top.2# Replacing solvent molecule 1163 (atom 6250) with NA+ and then nothing happens. genion.log gets generated only half way. My system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via synaptic and also built from source. The same thing happens in both of them. Gromacs version is 3.3.1. However, when I try the same thing on another machine, a HP Proliant ML350 with Debian Sarge and Gromacs 3.3.1, everything goes well. None of the gromacs programs gives any errors before genion. I'll give you more info about the system configuration if anyone asks :) Sampo ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [[gmx-users] genion error!]
Maybe you forgot to delete the waters that were removed in the ionization process? /Pär Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Fatal error: Too many LINCS warnings (10190) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations. If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. I don't know what happen ,could somebody tell me? Thank you very much! pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- * Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion error!
Qiang Zhong wrote: Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Hardly surprising... most gromacs warnings should be considered carefully. First the atom names in your .gro and .top files have to match those in the .atp files for the force field you're using. Then check the order and number of Na and Cl are correct. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion error!
On 2/28/2007 7:52 PM, Mark Abraham wrote: Qiang Zhong wrote: Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Hardly surprising... most gromacs warnings should be considered carefully. I think what Mark means is that in such case, you shall not continue to run mdrun without inspecting the warnings. First the atom names in your .gro and .top files have to match those in the .atp files for the force field you're using. Then check the order and number of Na and Cl are correct. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Hi Guys, I have a question. I am using genion to add two ZN2+ ions to a protein that already has two. I thought I would just use genion with np 2. However it seemed to recognize that there were already two in the file and added none. So instead I used the parameter np 4. This seemed to add two, for a total of four, which I wanted. However sometimes it seems to add two too many! Am I understanding the proper use of the np parameter? If it seemed to add two too many, then the most likely cause was that you had fewer ions in your input structure than you thought you had. You should check out the man page for genion, and consider using -pq. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GENION: Ions inside the protein
you might have deleted just one atom of water molecule. Ex: If you are using SPC water , you have to delete all 3 atoms in index file. Best way is to make changes in .gro file.. Renumber the resulting .gro file using genconf, make a new index file and start running. On 10/10/06, Una Bjarnadottir [EMAIL PROTECTED] wrote: Dear users,In some of my simulations after neutralizing the systems with genion 2of the ions were inside the active site cleft of the protein. In the discussion on the list it was commented to either delete thesolvent within the protein which I did I deleted the water molecule(11798) and gave genion that index file as input but than this error came: Fatal error: The solvent group is not continuous: index[8198]=11797,index[8199]=11799I don't want to use the -random command in genion if possible because innone of the other simulations I have used it. Is there any other way to delete the solvent within the protein did Imisunderstand that so those water molecules will not be replaced?Best regards, Una Bjarnadottir___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GENION: Ions inside the protein
Hi, The error message tries to make clear that genion can only replace water molecules in an index group without gaps. It has to be continuous. So the point that was made earlier on the list was that the water molecules should be deleted in the .gro file. Alternatively, they can also be moved to the beginning of the end of the solvent section and from the (renumbered) resulting file an index file can be constructed. Hope it helps, Tsjerk On 10/10/06, Viswanadham Sridhara [EMAIL PROTECTED] wrote: you might have deleted just one atom of water molecule. Ex: If you are using SPC water , you have to delete all 3 atoms in index file. Best way is to make changes in .gro file.. Renumber the resulting .gro file using genconf, make a new index file and start running. On 10/10/06, Una Bjarnadottir [EMAIL PROTECTED] wrote: Dear users, In some of my simulations after neutralizing the systems with genion 2 of the ions were inside the active site cleft of the protein. In the discussion on the list it was commented to either delete the solvent within the protein which I did I deleted the water molecule (11798) and gave genion that index file as input but than this error came: Fatal error: The solvent group is not continuous: index[8198]=11797, index[8199]=11799 I don't want to use the -random command in genion if possible because in none of the other simulations I have used it. Is there any other way to delete the solvent within the protein did I misunderstand that so those water molecules will not be replaced? Best regards, Una Bjarnadottir ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups
Una Bjarnadottir wrote: Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which is the last water atom (total in system 33003) and groups 15 and 1 are Cl and protein groups if I on the other hand do not neutralize the system the run goes fine! When looking into the .ndx file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14 (SOL) and 16 (other). How can I change the group definitions and make sure the groups do not overlap and to be unique? It seems to be something wrong with how the genion works for me. I followed the tutorial and chose the SOL group and water molecules were replaced by the Cl ions. Than I modifyed the .top file and took 3 sol molecules and added the 3 ions. Please help because have not been able to fix the problem with related letters on the subject on the list. Best regards, Una Bjarnadottir What do your tcoupl groups look like? Could it be System SOL? The number may be confusing, you should subtract one from them when compared to the output from gmxcheck -n index.ndx So it seems that atom 33000 (numbering in the coordinate file) is in groups 14 and 0. Maybe you should make a new index file after genion. Note that it is good practice to make the ions part of the solvent T coupling group. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups
Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) Read closely - T-Coupling group, not group. You choose the T-Coupling groups from among those in the .ndx file (or from the default groups in its absence, as you're doing here) and specify them in the .mdp file. Thus you should look there first of all. You need to use a disjoint set of T-Coupling groups, so this error is consistent with not having done that. If you were using .ndx file (which you aren't), it might be possible your .ndx file doesn't correspond to your post-genion structure and something weird happens. I'd expect GROMACS woud die with a more helpful error in such a case though. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion in gromacs 3.3.1
Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear colleagues, It looks like genion behaviour has changed in gromacs 3.3.1 as compared to 3.3 I still have both binaries in my machine and when using identical inputs to add some Na cations the new one (3.3.1) adds them randomly, while the previous one adds them at the most favorable electrostatic potential positions, as I intended to. I have looked in the (v. 3.3) documentation but I have failed to find a reason for this. Should I change something in my input file (or at the command line) in order to get genion from v.3.3.1 adding the cations non-randomly? You can try -norandom. I was under the impression that the potential based placement was broken (had been for a while). Thank you for your help, and sorry if it was a trivial question. Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEOl5BF6oOrDvhbQIRAoLKAJ95T0+5rROR3NADN5seOnmaihpDpwCeNLco E0gGQP2715f8SgzTt6LKCsA= =vP3d -END PGP SIGNATURE- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion in gromacs 3.3.1
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You can try -norandom. I was under the impression that the potential based placement was broken (had been for a while). Hi David, Thank you very much, the command line option -norandom did work and placed the cations in the same place as the older (3.3) version of genion. Well, I can tell for sure, but I am inclined to think that the cations are placed in reasonable positions. Sorry, I was useless at not having noticing the option in program description. Perhaps de default moved from 'norandom' to 'random' with the new version. Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEOnKCF6oOrDvhbQIRAoNtAJ0aBQA1ie+FkLno4NaK3zmq4xRuiwCeMoRJ X29pTe7GXNvCA86Ox2YA2QM= =ZB0D -END PGP SIGNATURE- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
