[gmx-users] Re: Calculation of water density around certain protein residues
Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg In the output, I got for each time step I some number of residues. For eg, @ s0 legend Nearby water 0.000 159.000 0.200 168.000 0.400 173.000 0.600 171.000 Can I get the average the number of water moleculed for the entire simulation time ?? and how can I get the density instead of number ?? Pls respond to this query ... Thanks -- Bharat -- 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] Different Residues...
Hello Dear GROMACS users, I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I get the following error: Fatal error: Residue '' not found in residue topology database I'm a beginner GROMACS user, but I want to know exactly, how add my residues to GROMACS step by step?. My residues contain S. Ramon.. -- 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] Fw: energy minimization problem
Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtol should be lower than 1. As I understand, you mean that for these systems emtol should be 0 or negative. Is it really true? Best Regards Kiana -- 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] TFE-water simulation
Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
That should be enough. You may want to use the -march (or equivalent) compiler flag for CPU optimization. Cheers, -- Szilárd Páll On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs Users! I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7 cpu with dual GeForces Titans gpu mounted. With this config I'd like to perform simulations using cpu as well as both gpus simultaneously. What flags besides cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5 should I define to CMAKE for compiling optimized gromacs on such workstation? Thanks for help James -- 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] gmxcheck
Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn't any file that I can see. I had run some simulations but now that I had to write a quick report about the parameters and essential things mentioned likewise in the methods section, I realized that I had not kept tab of the basic details so found out that gmxcheck does that but I haven't been successful. Any insight on this would be quite helpful. Kind regards -- Ankita Naithani -- 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] TFE-water simulation
Erratum: Where I wrote I ended up going with the former it should be I ended up going with the latter. /J On Mon, Nov 4, 2013 at 10:47 AM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0
Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create --no-recursion checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu ./configure: line 2050: syntax error near unexpected token `tar-ustar' ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' make: *** [config.status] Error 2 I have another query regarding the gromacs that comes with the Rocks cluster distribution. The mdrun of that gromacs has been complied without mpi option. How can I recomplie with mpi option. As I need the .configure file which is not there in the installed gromacs folder of the rocks cluster ... Thanks in advance for help Regards Bharat -- 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] Wall potential for a membrane simulation
Hello, I would like to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40xNa+) above the membrane and water and chloride ions (40 Cl-) beneath it. First, I built up the system, did an energy minimization and then implemented the walls for the npt-equilibration. I didn't change anything in the topology. (Do I have to define the wall-atom-type there?If yes, what exactly do I have to put in the topology?) The interesting part of my nvt.mdp file looks like that: nwall = 2 wall_type = 10-4 wall_density = 100 100 wall_atomtype = C C wall_r_linpot = 1 1 ; with -1 I got a fatal error, because atoms were beyond the wall wall_ewald_zfac = 3 ewald_geometry= 3dc pbc = xy; Periodic Boundary Conditions in x/y direction What I see in VMD is the following: as expected some NA-ions are going through the membrane to reach the chloride/water side. But at the same time water molecules (and one chloride-ion) at both sides disappear in z-direction and never come back. In the first 10ps (with a tiny time step of 0.1fs) there were only a few molecules that went outside the box, but after 10 ps it increased dramatically and at some point the equilibration crashed. I already played around with time-steps, atom-types and the density, but couldn't find anything that works to keep the molecules inside the box... Anyone has an idea what I did wrong and how I can correct it? Unfortunately there is not much about that in the manual and I could not find anything that really helped me in the mailing-list archive Thanks in advance!!! Cheers, Marianne Schulte -- 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] Calculation of water density around certain protein residues
Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg In the output, I got for each time step I some number of residues. For eg, @ s0 legend Nearby water 0.000 159.000 0.200 168.000 0.400 173.000 0.600 171.000 Can I get the average the number of water moleculed for the entire simulation time ?? and how can I get the density instead of number ?? Pls respond to this query ... Thanks -- Bharat -- 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] Fwd: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0
Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create --no-recursion checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu ./configure: line 2050: syntax error near unexpected token `tar-ustar' ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' make: *** [config.status] Error 2 I have another query regarding the gromacs that comes with the Rocks cluster distribution. The mdrun of that gromacs has been complied without mpi option. How can I recomplie with mpi option. As I need the .configure file which is not there in the installed gromacs folder of the rocks cluster ... Thanks in advance for help Regards Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
Szilárd, thanks for suggestion! What kind of CPU optimisation should I take into account assumint that I'm using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12 nodes in Debian). James 2013/11/4 Szilárd Páll pall.szil...@gmail.com That should be enough. You may want to use the -march (or equivalent) compiler flag for CPU optimization. Cheers, -- Szilárd Páll On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs Users! I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7 cpu with dual GeForces Titans gpu mounted. With this config I'd like to perform simulations using cpu as well as both gpus simultaneously. What flags besides cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5 should I define to CMAKE for compiling optimized gromacs on such workstation? Thanks for help James -- 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] DPOSRES and energy minimization
On 11/4/13 1:31 AM, Gianluca Interlandi wrote: Is there a way to tell from the log file whether positional restraints are really activated or not? Yes, there is a position restraint energy term written to the .log and .edr files if the restraints are active. -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] g_lie useage
On 11/4/13 1:52 AM, Saman Shahriyari wrote: dear gmx users i am trying to use g_lie tool regarding the fact i am a newbie to this. so i searched through the web for an appropriate protocol. although there are lots of staffs discussing the theory, but i couldn't find any thing describing the steps techniqally and with some details. generally speaking, this is what seemed to me as the steps that i need to go through (it would be the kind of you to help me know if they are correct and what is missing): 1-runnig two md simulations for free and bond ligand (using PME) 2- doing the mdrun with -rerun flag by using the new .mdp (as is prepared in gmx forum: http://gromacs.5086.x6.nabble.com/Doubts-over-g-lie-usage-td5000130.html) and the old .tpr file. Do not use the old .tpr file. If you make changes to the .mdp file, then they will not take effect unless you re-run grompp and use the new .tpr file. -Justin 3- using g-energy to extract Elj and Eqq from ligand simulation in water (using the outputs of step 2 ) 4- using the g-lie command by introducing Elj and Eqq to it, in order to have the final free energies of binding. i do appreciate your kind help saman -- == 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] Different Residues...
On 11/4/13 3:16 AM, Ramon Valencia wrote: Hello Dear GROMACS users, I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I get the following error: Fatal error: Residue '' not found in residue topology database I'm a beginner GROMACS user, but I want to know exactly, how add my residues to GROMACS step by step?. My residues contain S. The fact that pdb2gmx is finding a blank residue indicates that your input file format is badly broken. -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] Fw: energy minimization problem
On 11/4/13 3:29 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtol should be lower than 1. As I understand, you mean that for these systems emtol should be 0 or negative. Is it really true? I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2013-November/085136.html -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] gmxcheck
On 11/4/13 5:06 AM, Ankita Naithani wrote: Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn't any file that I can see. You need to provide a .tpr file, as well. I had run some simulations but now that I had to write a quick report about the parameters and essential things mentioned likewise in the methods section, I realized that I had not kept tab of the basic details so found out that gmxcheck does that but I haven't been successful. The output from gmxcheck will be of little use, in my opinion. All it does is write some chosen .mdp settings in full sentences, which does not give you a complete description of all the relevant settings. -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] gmxcheck
Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any suggestions to recover the essential information which you would include as part of methods? Kind regards, Ankita On Mon, Nov 4, 2013 at 12:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 5:06 AM, Ankita Naithani wrote: Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn't any file that I can see. You need to provide a .tpr file, as well. I had run some simulations but now that I had to write a quick report about the parameters and essential things mentioned likewise in the methods section, I realized that I had not kept tab of the basic details so found out that gmxcheck does that but I haven't been successful. The output from gmxcheck will be of little use, in my opinion. All it does is write some chosen .mdp settings in full sentences, which does not give you a complete description of all the relevant settings. -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 -- Ankita Naithani -- 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] gmxcheck
On 11/4/13 7:14 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any There are no frames in a .tpr file. I suspect you're simply issuing the command incorrectly, but since you haven't shown us what you're doing, there's little else to suggest. suggestions to recover the essential information which you would include as part of methods? The .mdp file has all the instructions for the simulation. If you don't have that around for whatever reason (very bad to get rid of such files!), all of the same information is recorded in the beginning of the .log file or can be written out by gmxdump. In the latter case, make sure to redirect the output to a file rather than just have thousands of lines of text blur by in the terminal. -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] gmxcheck
I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 7:14 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any There are no frames in a .tpr file. I suspect you're simply issuing the command incorrectly, but since you haven't shown us what you're doing, there's little else to suggest. suggestions to recover the essential information which you would include as part of methods? The .mdp file has all the instructions for the simulation. If you don't have that around for whatever reason (very bad to get rid of such files!), all of the same information is recorded in the beginning of the .log file or can be written out by gmxdump. In the latter case, make sure to redirect the output to a file rather than just have thousands of lines of text blur by in the terminal. -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 -- Ankita Naithani -- 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] gmxcheck
On 11/4/13 7:37 AM, Ankita Naithani wrote: I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? Yes, buried in a long list of other things. Trivial details like that are simply read from the last few lines of the .top though, so there's no need to invoke any other accessory programs. -Justin On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 7:14 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any There are no frames in a .tpr file. I suspect you're simply issuing the command incorrectly, but since you haven't shown us what you're doing, there's little else to suggest. suggestions to recover the essential information which you would include as part of methods? The .mdp file has all the instructions for the simulation. If you don't have that around for whatever reason (very bad to get rid of such files!), all of the same information is recorded in the beginning of the .log file or can be written out by gmxdump. In the latter case, make sure to redirect the output to a file rather than just have thousands of lines of text blur by in the terminal. -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 -- == 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] Re: Hardware for best gromacs performance?
just a small benchmark... each node - 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs 42827 atoms - vsites - 4fs 1 node142 ns/day 2 nodes FDR14 218 ns/day 4 nodes FDR14 257 ns/day 8 nodes FDR14 326 ns/day 16 nodes FDR14 391 ns/day (global warming) best, timo -- 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] gmxcheck
Thanks Justin very much for your help. (Extremely silly and unthoughtful of me to forget this) Kind regards, Ankita On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 7:37 AM, Ankita Naithani wrote: I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? Yes, buried in a long list of other things. Trivial details like that are simply read from the last few lines of the .top though, so there's no need to invoke any other accessory programs. -Justin On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 7:14 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any There are no frames in a .tpr file. I suspect you're simply issuing the command incorrectly, but since you haven't shown us what you're doing, there's little else to suggest. suggestions to recover the essential information which you would include as part of methods? The .mdp file has all the instructions for the simulation. If you don't have that around for whatever reason (very bad to get rid of such files!), all of the same information is recorded in the beginning of the .log file or can be written out by gmxdump. In the latter case, make sure to redirect the output to a file rather than just have thousands of lines of text blur by in the terminal. -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 -- == 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 -- Ankita Naithani -- 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] Fw: energy minimization problem
Dear Justin It is obvious that emtol value can not be zero or negative. but you wrote in your email For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and in double precision. what did you mean by saying emtol1? Anyway, my question was: for free energy calculation in double precision, what should be the best value for emtol? Best Regards Kiana On Monday, November 4, 2013 3:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 3:29 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtol should be lower than 1. As I understand, you mean that for these systems emtol should be 0 or negative. Is it really true? I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2013-November/085136.html -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] Fw: energy minimization problem
On 11/4/13 8:55 AM, kiana moghaddam wrote: Dear Justin It is obvious that emtol value can not be zero or negative. but you wrote in your email For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and in double precision. what did you mean by saying emtol1? Anyway, my I mean exactly what I said. You should set emtol to some value of 1 or less as a target for NMA. question was: for free energy calculation in double precision, what should be the best value for emtol? I have not worked with systems that have required such strenuous minimization, but I believe the general recommendation (if necessary for whatever you're working with, and I'm not prepared to try to guess about what you're doing) is to minimize as far as you possibly can. Set some very low value of emtol and some very high value of nsteps and let the EM algorithms churn away. You will usually need several rounds of EM using different methods to achieve this. Published literature and previous posts to this list (in the archive) should be sufficient to guide you. -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] Re: Hardware for best gromacs performance?
Brad, These numbers seems rather low for a standard simulation setup! Did you use a particularly long cut-off or short time-step? Cheers, -- Szilárd Páll On Fri, Nov 1, 2013 at 6:30 PM, Brad Van Oosten bv0...@brocku.ca wrote: Im not sure on the prices of these systems any more, they are getting dated so they will be on the low end price wise. I have a 30,000 ish atom lipid system for all my simulations so this might be helpful: System 1 CPU - dual 6 core xeon @ 2.8 GHz GPU - 2x GTX 680 50 ns/day System 2 CPU - dual 4 core intel E5607 @ 2.26 GHz GPU - 2x M2070 45 ns/day System 3 CPU - dual 4 core intel E5620 @ 2.40 GHz GPU - 1x GTX 680 40 ns/day -- View this message in context: http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012152.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Hardware for best gromacs performance?
Hi David, Do you want to maximize throughput with multiple simulations or you want single simulations as fast as possible? In general, as few and fast CPU(s)/GPU(s) is best - especially with such small systems as yours which won't scale very well to more than 1-2 GPUs. As I previously mentioned on the list, your budget option is a fast Intel desktop (i7) CPU with a GTX 680/770/780 GPU, the pricey one is to go with a dual-socket server/workstation machine and 2xTITAN GPUs. NVIDIA partners has a free test drive program which may be useful for you to try out a few machine configurations before buying. (Note that I have never tried it myself, so I can't provide more details or vouch for it in any way.) Cheers, -- Szilárd Páll On Fri, Nov 1, 2013 at 3:08 AM, David Chalmers david.chalm...@monash.edu wrote: Hi All, I am considering setting up a small cluster to run Gromacs jobs. The aim would be to maximise ns/day/$ for smallish systems of 15-30,000 atoms. Can anybody provide advice/benchmarks/anecdotes about what type of current hardware provides the best performance/price? Would it be something like a dual core xeon system with two (or more?) Titan GPUs? Thanks David --- David Chalmers Senior Lecturer Faculty of Pharmacy and Pharmaceutical Sciences Medicinal Chemistry Monash Institute of Pharmaceutical Sciences Monash University (Parkville campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: +61 3 9903 9110 Fax: +61 3 9903 9582 -- 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] Gromacs-4.6 on two Titans GPUs
You can use the -march=native flag with gcc to optimize for the CPU your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge CPUs. -- Szilárd Páll On Mon, Nov 4, 2013 at 12:37 PM, James Starlight jmsstarli...@gmail.com wrote: Szilárd, thanks for suggestion! What kind of CPU optimisation should I take into account assumint that I'm using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12 nodes in Debian). James 2013/11/4 Szilárd Páll pall.szil...@gmail.com That should be enough. You may want to use the -march (or equivalent) compiler flag for CPU optimization. Cheers, -- Szilárd Páll On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs Users! I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7 cpu with dual GeForces Titans gpu mounted. With this config I'd like to perform simulations using cpu as well as both gpus simultaneously. What flags besides cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5 should I define to CMAKE for compiling optimized gromacs on such workstation? Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta bharat.85.m...@gmail.comwrote: Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make These is no need to run make as root - doing so guarantees you have almost no knowledge of the final state of your entire machine. /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create --no-recursion checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu ./configure: line 2050: syntax error near unexpected token `tar-ustar' ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' make: *** [config.status] Error 2 Looks like the system has an archaic autotools setup. Probably you can comment out the line with tar-ustar from the original configure script, or remove tar-ustar. Or use the CMake build. I have another query regarding the gromacs that comes with the Rocks cluster distribution. The mdrun of that gromacs has been complied without mpi option. How can I recomplie with mpi option. As I need the .configure file which is not there in the installed gromacs folder of the rocks cluster ... The 4.5-era GROMACS installation instructions are up on the website. Whatever's distributed with Rocks is more-or-less irrelevant. Mark Thanks in advance for help Regards Bharat -- 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] Group protein not found in indexfile
Hello I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.chainX.itp. When I use grompp however, I get a fatal error “Group protein not found in index file. Maybe you have non-default groups in your .mdp file, while not using ‘-n’ option in grompp” I’ve looked up this error on-line but I don’t see people getting this error when using multiple chains. I only have protein present and nothing else. I am obviously doing something incorrect. I would greatly appreciate any comments that would help me.. Thanks. -- 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] Analysis tools and triclinic boxes
Dear all, I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail list, it is my understanding that the default box shape in gromacs in a triclinic box. Can I assume that all the analysis tools also work for a triclinic box. Cheers, Stephanie -- 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] Group protein not found in indexfile
On 11/4/13 1:29 PM, Steve Seibold wrote: Hello I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.chainX.itp. When I use grompp however, I get a fatal error “Group protein not found in index file. Maybe you have non-default groups in your .mdp file, while not using ‘-n’ option in grompp” I’ve looked up this error on-line but I don’t see people getting this error when using multiple chains. I only have protein present and nothing else. I am obviously doing something incorrect. I would greatly appreciate any comments that would help me.. Please provide: 1. Your exact grompp command 2. Your full .mdp file 3. The gmxcheck output of the .ndx file -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] Analysis tools and triclinic boxes
On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote: Dear all, I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail list, it is my understanding that the default box shape in gromacs in a triclinic box. Can I assume that all the analysis tools also work for a triclinic box. All analysis tools should work correctly for all box types. Is there a specific issue you are having, or just speculation? -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] TFE-water simulation
Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -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 -- 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] Gentle heating with implicit solvent
Dear Mark, Sorry for replying to an older thread. We are trying to perform implicit solvent simulations of protein G with CHARMM27 in gromacs. We are trying to trouble shoot why the protein unfolds after already 2 ns of dynamics. We use simulated annealing for the heating with 1 fs time step. The thermostat is v_rescale and OBC is the GBSA algorithm. Do you have any suggestions what we could improve? You mention using a sub-fs time step for the equilibration. Do you still use LINCS? Do you use simulated annealing to heat up the system or do you just apply position restraints to the heavy atoms? Thanks, Gianluca On Wed, 28 Aug 2013, Mark Abraham wrote: It can be. Lack of explicit degrees of freedom of solvent can make achieving equipartition tricky. With CHARMM27 and virtual sites in implicit solvent, I have sometimes found it necessary to use a sub-femtosecond time step at the start of equilibration, even where there were no atomic clashes. Maybe the system was just unlucky with generating velocities, though :-) Mark On Aug 28, 2013 7:16 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: How important is it to do gentle heating (using simulated annealing) with GBSA? Often with explicit water it is enough to perform some equilibration with positional restraints. Would it be enough to do the same with implicit solvent? Thanks, Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- 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] Group protein not found in indexfile
Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. Thanks again, Stevegrompp -f pr.mdp -n pr.ndx -c prbox.pdb -p system.top -o pr.tpr -- 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] Group protein not found in indexfile
On 11/4/13 3:03 PM, Steve Seibold wrote: Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. The list does not accept attachments, nor do I need any actual files. Please provide the gmxcheck output on the index file (copied and pasted), and copy and paste your .mdp text into a reply email. -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] Gentle heating with implicit solvent
On 11/4/13 2:25 PM, Gianluca Interlandi wrote: Dear Mark, Sorry for replying to an older thread. We are trying to perform implicit solvent simulations of protein G with CHARMM27 in gromacs. We are trying to trouble shoot why the protein unfolds after already 2 ns of dynamics. We use simulated annealing for the heating with 1 fs time step. The thermostat is v_rescale and OBC is the GBSA algorithm. Do you have any suggestions what we could improve? You mention using a sub-fs time step for the equilibration. Do you still use LINCS? Do you use simulated annealing to heat up the system or do you just apply position restraints to the heavy atoms? A complete .mdp file would be helpful. Are you using finite cutoffs? -Justin Thanks, Gianluca On Wed, 28 Aug 2013, Mark Abraham wrote: It can be. Lack of explicit degrees of freedom of solvent can make achieving equipartition tricky. With CHARMM27 and virtual sites in implicit solvent, I have sometimes found it necessary to use a sub-femtosecond time step at the start of equilibration, even where there were no atomic clashes. Maybe the system was just unlucky with generating velocities, though :-) Mark On Aug 28, 2013 7:16 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: How important is it to do gentle heating (using simulated annealing) with GBSA? Often with explicit water it is enough to perform some equilibration with positional restraints. Would it be enough to do the same with implicit solvent? Thanks, Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- == 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
[gmx-users] .top file for a mixed solvent
Hi gmx users, I want to simulate ionomer is mixed solution of water and ethanol using gromos force field. I tired to follow the steps suggested on gromacs website, which are: 1- Determine the number of co-solvent molecules necessary, given the box dimensions of your system. 2- Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro). 3- Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box. 4- Fill the remainder of the box with water (or whatever your other solvent is) using genbox. 5- Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system. Here are the commands that I used: pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top -i ionomer4.itp (ionomer-4.pdb is the pdb file for 4 ionomer molecule) pdb2gmx -f eth.pdb -o eth.gro -p eth.top -i eth.itp (eth.pdb is the pdb file for single ethanol molecule) editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -ci eth.gro -nmol 1000 -o phase1.gro genbox -cp phase1.gro -cs spc216.gro -o solvated.gro At the end, I have the solvated.gro file with 4 ionomer, 396 ethanol, and 423 water molecules. I don't know how to proceed step 5 and generated a combine .top file. What should I do with [ molecules ] directive? I appreciate any suggestions. Kind regards, Ehsan -- 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] Different Residues...
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Ramon Valencia Sent: Monday, 4 November 2013 7:17 PM To: gmx-users@gromacs.org Subject: [gmx-users] Different Residues... Hello Dear GROMACS users, I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I get the following error: Fatal error: Residue '' not found in residue topology database I'm a beginner GROMACS user, but I want to know exactly, how add my residues to GROMACS step by step?. My residues contain S. Ramon.. -- 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] Calculation of water density around certain protein residues
You have a number of molecules, you know what those molecules are, you can calculate their mass, you know the volume, therefore you can calculate a density. For the average for entire simulation, simply pass the water.xvg file to g_analyze There is all the information you require right there in what you have already. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of bharat gupta Sent: Monday, 4 November 2013 10:33 PM To: Discussion list for GROMACS users Subject: [gmx-users] Calculation of water density around certain protein residues Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg In the output, I got for each time step I some number of residues. For eg, @ s0 legend Nearby water 0.000 159.000 0.200 168.000 0.400 173.000 0.600 171.000 Can I get the average the number of water moleculed for the entire simulation time ?? and how can I get the density instead of number ?? Pls respond to this query ... Thanks -- Bharat -- 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] .top file for a mixed solvent
On 11/4/13 5:25 PM, Ehsan Sadeghi wrote: Hi gmx users, I want to simulate ionomer is mixed solution of water and ethanol using gromos force field. I tired to follow the steps suggested on gromacs website, which are: 1- Determine the number of co-solvent molecules necessary, given the box dimensions of your system. 2- Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro). 3- Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box. 4- Fill the remainder of the box with water (or whatever your other solvent is) using genbox. 5- Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system. Here are the commands that I used: pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top -i ionomer4.itp (ionomer-4.pdb is the pdb file for 4 ionomer molecule) pdb2gmx -f eth.pdb -o eth.gro -p eth.top -i eth.itp (eth.pdb is the pdb file for single ethanol molecule) editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -ci eth.gro -nmol 1000 -o phase1.gro genbox -cp phase1.gro -cs spc216.gro -o solvated.gro At the end, I have the solvated.gro file with 4 ionomer, 396 ethanol, and 423 water molecules. I don't know how to proceed step 5 and generated a combine .top file. What should I do with [ molecules ] directive? List the number of ETH and SOL, respectively, in whatever order they appear in the coordinate file. You need to have #included the relevant .itp files for ethanol and water in the ionomer .top beforehand. The water .itp file was probably added by pdb2gmx. -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] Gentle heating with implicit solvent
Hi Justin, We are using infinite cutoffs (all vs all). Here is the mdp file for the heating (please note that -DPOSRES is commented out) and the time step is 1 fs: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = ;define = -DPOSRES ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 bd-fric = 0 ld_seed = 1993 ; IMPLICIT SOLVENT OPTIONS = implicit-solvent = GBSA gb-algorithm = OBC rgbradii = 0 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 100 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 0 ; ns algorithm (simple or grid) = ns_type = simple ; Periodic boundary conditions: xyz or no = pbc = no ; nblist cut-off = rlist= 0 ;rlistlong= 1.8 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Cut-off rcoulomb_switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths= rvdw_switch = 0 rvdw = 0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = V-rescale ; Groups to couple separately = tc_grps = Protein ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 ref_t= 300 ; Pressure coupling = Pcoupl = no Pcoupltype = isotropic refcoord_scaling = All ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; SIMULATED ANNEALING CONTROL = annealing= single ; Number of time points to use for specifying annealing in each group annealing_npoints = 21 ; List of times at the annealing points for each group annealing_time= 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 ; Temp. at each annealing point, for each group annealing_temp= 5 30 30 60 60 90 90 120 120 150 150 180 180 210 210 240 240 270 270 300 300 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 5 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = ;constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Use successive overrelaxation to reduce the number of shake iterations = Shake-SOR= no ; Relative tolerance of shake = shake_tol= 1e-04 ; Highest order in the expansion of the constraint coupling matrix =
[gmx-users] Re: Using gromacs on Rocks cluster
Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ?? -- Bharat -- 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] Fwd: Using gromacs on Rocks cluster
Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ?? -- Bharat -- 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] choosing force field
Dear all I would like to carry out unfolding simulations of my dimeric protein and would like to know which is the better force field to work with out of gromos 96 43 or 53? Also, is gromos 96 43a1 force field redundant? When I searched the previous archive, I could see similar question was raised for gromos 96 43a3 ff and could make out that 53a6 53a7..have entirely different approach in parameterization compared to 43a3 ff. Also 43a3 would give more stable structures. So is the case with my simulations but with force field 43a1 (instead of 43a3). I could see an extra non native helix when I carried out simulations with ff 43a1 which is not present with 53a7 ff. I have no experimental data/re-sources to confirm this. Also simulations on my system has not been done before. I would like to know which out of the two simulations should I consider more reliable-43a1 or 53a7? Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Diffusion/PBC
Dear All, I have an problem related to jumping trajectory. In my MD run, there is a receptor molecule which is binding with an halogen anion in water solvent. In the original trajectory, the binding between them looks fine but jumping present. To remove the jumping of the system from trajectory, I have used 'nojump' as discussed in the forum. Now I got a jump-free trajectory, but due to the diffusion here, I have observed that the anion and the receptor are far away from each other. I could not fix the problem. can any one suggest me? Thanks in advance. with regards, *Debashis Sahu* *Central Salt and Marine Chemical Research Institute* *Bhavnagar, Gujarat* *India, 364002.* -- 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
