[gmx-users] Fwd: g-dist
-- Forwarded message -- From: mohsen ramezanpour ramezanpour.moh...@gmail.com Date: Sat, Dec 25, 2010 at 5:09 PM Subject: g-dist To: Discussion list for GROMACS users gmx-users@gromacs.org Dear All How can we measure the distance between COM of two molecules?of course in vector form! 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] Fwd: pulling
-- Forwarded message -- From: mohsen ramezanpour ramezanpour.moh...@gmail.com Date: Sat, Dec 25, 2010 at 10:02 AM Subject: pulling To: Discussion list for GROMACS users gmx-users@gromacs.org Dear All I want to pull my ligand from protein which is docked to it for generating configurations for umbrella sampling. But my ligand is located in a hole inside of protein. If I pull it along the line which is connecting COMs of them,the ligand may be arrested(constraint)inside of hole. Am I force to pull ligand along this line or I can pull along any line for generating configurations for umbrella sampling? I think the important is to pull it out from the binding pocket and we need to pull it along a line which is connecting the center of pocket(no protein's COM)to ligand's COM. What do you think. 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] topolbuild1_3 install problem
Hi, Mark, Thanks for the reply. You'are right,I forgot to enter the path.And my computer system is Ubuntu 10.04.I want to use the glycam force filed, then I type the command: software/topolbuild1_3/src/topolbuild -h I got the correct help information. But when I type this integral command: software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename it's error: *...@ubuntu:~$ software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename Fatal error. Source code file: atom_types.c, line: 87 Cannot open file software/topolbuild1_3/src/dat/parm/dat/antechamber/ATOMTYPE_GLYCAM.DEF Do you know how to solve this problem ? Thanks for you reply! xiaodu -- 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-dist
Hi Mohsen,
I think you'll have to get a bit creative with g_traj to get the COMs,
followed by either some simple scripting or nifty usage of paste and awk
(something like: paste com1.xvg com2.xvg | awk '/^...@#;]/{print $2-$6,
$3-$7, $4-$8}').
Hope it helps,
Tsjerk
On Dec 25, 2010 2:40 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com
wrote:
Dear All
How can we measure the distance between COM of two molecules?of course in
vector form!
thanks in advance
--
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Re: [gmx-users] topolbuild1_3 install problem
On Sun, December 26, 2010 at 6:07 AM, gromacs564 gromacs...@126.com wrote: I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I write export PATH=$PATH:/home/buct/topolbuild1_3 into etc/profile(root) ``` But When I type topolbuild -h I get command not found,and I don't know how to deal it. can anyone tell me to install the topolbuild1_3 correctly? First, I hope that you mean that you changed directory to home/buct/topolbuild1_3/src before giving the make command since Makefile is in src and not in the main directory which means that giving the make command in any other directory should give an error message. Second, the topolbuild binary will be in home/buct/topolbuild1_3/src after the build, but the commands you give search home/buct/topolbuild1_3 for an executable where there shouldn't be an executable. Third, the text files, in the main directory, home/buct/topolbuild1_3 do include installation and use information. Please see in particular INSTALLATION.txt and README.txt Fourth, the resulting topology from topolbuild 1.* works with gromacs 3.3.3 and gromacs 4.0.*, but the rearrangement of the force field files with gromacs 4.5.* means that the include file lines for such a topology will need minor editing with a text editor to be usable with gromacs 4.5.*One example of such editing has been posted. The 2.0 version of topolbuild will be designed for gromacs 4.5.*. I hope this helps you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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] topolbuild1_3 install problem
On Mon, December 27, 2010 at 5:02 AM, gromacs564 gromacs...@126.com wrote: Hi, Mark, Thanks for the reply. You'are right,I forgot to enter the path.And my computer system is Ubuntu 10.04.I want to use the glycam force filed, then I type the command: software/topolbuild1_3/src/topolbuild -h I got the correct help information. But when I type this integral command: software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename it's error: *...@ubuntu:~$ software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename Fatal error. Source code file: atom_types.c, line: 87 Cannot open file software/topolbuild1_3/src/dat/parm/dat/antechamber/ATOMTYPE_GLYCAM.DEF Do you know how to solve this problem ? Thanks for you reply! The problem is that you are giving the wrong directory after -dir The -dir parameter entry is supposed to point to the directory that contains the dat directory because it needs the atom types file as well as the leap parameters file Try instead: software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3 -ff glycam06_c -r MAL -rename I hope this helps as well. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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] Energy due to Hydrogen bonds
Hi ALL, Is there any means to calculate the total energy arising due to the breaking and formation for hydrogen bonds only in GROMACS? Does the .edr file contains this information? If yes then how to parse it? I don't think the .log file records this value. Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Energy due to Hydrogen bonds
Anirban Ghosh wrote: Hi ALL, Is there any means to calculate the total energy arising due to the breaking and formation for hydrogen bonds only in GROMACS? Does the .edr file contains this information? If yes then how to parse it? I don't think the .log file records this value. Any suggestion is welcome. Discrete hydrogen bond energies are not part of any force field in Gromacs, so you will not find such terms in any file. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Potential Energy = -nan
hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DSTRONG_POSRES earlier when i was using ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DFLEXIBLE then problem was same help me ! with regards: shikha -- 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] Potential Energy = -nan
shikha agarwal wrote: hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DSTRONG_POSRES earlier when i was using ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DFLEXIBLE then problem was same Which version of Gromacs? On what hardware? I discovered a platform-specific bug that looked a lot like this, but I hesitate to suggest that until I know more. In all likelihood, you simply have unresolvable atomic overlap (i.e., you're packing too much) such that energy minimization cannot complete, since nan = not a number, or something is infinitely large or small. -Justin help me ! with regards: shikha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 76, Issue 59
From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Thu, August 12, 2010 2:32:17 AM Subject: gmx-users Digest, Vol 76, Issue 59 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. g_rms question (udi) 2. mdrun : error (Nilesh Dhumal) 3. Re: mdrun : error (Justin A. Lemkul) 4. need help (Anamika Awasthi) 5. Re: need help (Mark Abraham) 6. Re: g_rms question (Tsjerk Wassenaar) 7. trying to install gromacs on linux single processor (Anamika Awasthi) -- Message: 1 Date: Thu, 12 Aug 2010 00:39:03 +0300 From: udi udi_...@012.net.il Subject: [gmx-users] g_rms question To: gmx-users@gromacs.org Message-ID: 01cb399d$9e2dee10$da89ca...@net.il Content-Type: text/plain; charset=us-ascii Hi gromacs users, I'm simulating a protein that consists of 5 domains. I have calculated the whole protein's backbone RMSD by entering '4' twice. Now, I would like to calculate the contribution of every domain i.e. if the whole protein's RMSD in the first frame is 1nm, then how is this 1nm distributed between the 5 domains. I have created 5 groups in the index file of the backbone of every domain and calculated the RMSD by first entering '4' in order to fit the whole backbone and entered the domains backbone groups in the second entry. (5 different calculations). The problem is that the values I get from the domains do not add up to the whole backbone RMSD values!!! What am doing wrong? Thanks from advanced Chears Udi -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100812/e2049fd7/attachment-0001.html -- Message: 2 Date: Wed, 11 Aug 2010 20:43:05 -0400 From: Nilesh Dhumal ndhu...@andrew.cmu.edu Subject: [gmx-users] mdrun : error To: gmx-users@gromacs.org Message-ID: 9bfc32c21b990b64977354fe7b803a7c.squir...@webmail.andrew.cmu.edu Content-Type: text/plain;charset=iso-8859-1 Hello, I am trying to do equilibration for my system (solvent + solute). I am geting the following error. If I run solvent and solute molecules separately, its run well. For mixture I am getting following error. What this error means. Fatal error: 1 of the 22334 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck NIlesh -- Message: 3 Date: Wed, 11 Aug 2010 20:48:52 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] mdrun : error To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c6344f4.8020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Nilesh Dhumal wrote: Hello, I am trying to do equilibration for my system (solvent + solute). I am geting the following error. If I run solvent and solute molecules separately, its run well. For mixture I am getting following error. What this error means. Fatal error: 1 of the 22334 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Search the list archive. This has been asked and answered several times, so you'll likely find something useful. Also, take mdrun's advice and read about the options it's telling you. -Justin NIlesh -- 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 -- Message: 4 Date: Thu, 12 Aug 2010 12:09:50 +0530 From: Anamika Awasthi aawasth...@gmail.com Subject: [gmx-users] need help To: gmx-users@gromacs.org Message-ID: aanlktinqnjmg=z626t6xuam4rvrp+zc01stohw2+7...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear gromacs user, I want to install gromacs new version on my linux system. can u all please guide me, Thanking u in advance Anamika -- next part -- An HTML attachment was scrubbed... URL:
[gmx-users] Fwd: pulling
Dear mohsen: In US, there is no need to apply the force based on the COM. You can select any reaction coordinate that you want. Be sure that the reaction coordinate is not changing over time though (the COM is particularly refractory to this, which is probably why it is used, in addition to the COM being conceptually simple). The good news is that you check this like you check every convergence issue is US -- by block averaging your data and ensuring that there is no drift over time. Note though that US is not the only method to get binding free energies and you might want to try free energy perturbation with the gromacs free energy code instead of using the gromacs pull code to do US. Chris. -- original message -- Dear All I want to pull my ligand from protein which is docked to it for generating configurations for umbrella sampling. But my ligand is located in a hole inside of protein. If I pull it along the line which is connecting COMs of them,the ligand may be arrested(constraint)inside of hole. Am I force to pull ligand along this line or I can pull along any line for generating configurations for umbrella sampling? I think the important is to pull it out from the binding pocket and we need to pull it along a line which is connecting the center of pocket(no protein's COM)to ligand's COM. What do you think. Thanks in advance -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101227/a4bbf853/attachment-0001.html -- 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] glycam force field problem
Hi OliverI'm sorry to reply you so later.And I have some questions after reading your letter.You said that “The fudgeLJ under defaults should be 1.0 for GLYCAM“ and ”When you run grompp check in theoutput that fudge is set to 1.0.” Do you means to setting the fudgeLJ value to 1.0 in em.tpr file？I am not sure.I want to change this gromacs top files( all the output files by amb2gmx.pl converted) to gromacs itp files,then included in protein top file. And I plan to use the amber03 force filed. But I think that the [ defaults ] cannot included in itp files,or will cause an error about redifiniton.Because the [ defaults ] had exist in ”forcefield.itp.--;myt.itp [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5（ =1.0 ? ） 0.8333#define _FF_AMBER #define _FF_AMBER03 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333--So，do you know how to slove this problem？Can you give me some suggestion or a correct copy file by amb2gmx.pl converted? Thank you very much.My email address：gromacs...@126.comxiaodu -- 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] Potential Energy = -nan
hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DSTRONG_POSRES earlier when i was using ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DFLEXIBLE then problem was same Which version of Gromacs? On what hardware? I discovered a platform-specific bug that looked a lot like this, but I hesitate to suggest that until I know more. In all likelihood, you simply have unresolvable atomic overlap (i.e., you're packing too much) such that energy minimization cannot complete, since nan = not a number, or something is infinitely large or small. -- 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] Potential Energy = -nan
shikha agarwal wrote: hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . What is the hardware type? PowerPC, Intel 32- or 64-bit, etc? when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. Do other simple systems work? Can you do simple tutorial systems like lysozyme in water? Otherwise, you've got some topology problem that prevents the system from being properly minimized. Set nstxout=1 in your .mdp file and watch what's happening. -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
[gmx-users] coarse grainig with Martini ff???
ßÞ7~˪}ëÏxç^xÓnöÛ]5Ó Dear All I asked this question in Martini's forum, but tile now no answer, so I had to ask it here. excuse me.I did an atomistic peptide simulation. The residues and positions of all atoms in this peptide created by my self, I mean I didn't download the pdb file from www.pdb.org. at the end of atomistic simulation I have .pdb and .gro files that show the minimized structure of the peptide. Now I have a question: Can I use the last pdb file for a CG peptide? Can I use atom2cg.awk and seq2itp.pl in this case? Thank you Kargar-- 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] MPIRUN on Ubontu
Hi all, I have recently installed Ubonto on my computer (i5 processor) and installed gromacs 4.0.7. I have installed openmpi and fftw but when using mpirun command instead of getting parallel processes it simply runs the same job four times simultaneously. How do I make the necessary adjustments. Thanks, Gideon -- 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] Potential Energy = -nan
hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . Intel 32. I can perform simple task . I m trying nstxout=1 in my .mdp file. I will report u later. What is the hardware type? PowerPC, Intel 32- or 64-bit, etc? when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. Do other simple systems work? Can you do simple tutorial systems like lysozyme in water? Otherwise, you've got some topology problem that prevents the system from being properly minimized. Set nstxout=1 in your .mdp file and watch what's happening. -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] coarse grainig with Martini ff???
Faezeh Kargar wrote: Dear All I asked this question in Martini's forum, but tile now no answer, so I had to ask it here. excuse me. I did an atomistic peptide simulation. The residues and positions of all atoms in this peptide created by my self, I mean I didn't download the pdb file from www.pdb.org. at the end of atomistic simulation I have .pdb and .gro files that show the minimized structure of the peptide. Now I have a question: Can I use the last pdb file for a CG peptide? Can I use atom2cg.awk and seq2itp.pl in this case? You can run those scripts on any syntactically-correct .pdb file. -Justin Thank you Kargar -- 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] MPIRUN on Ubontu
גדעון לפידות wrote: Hi all, I have recently installed Ubonto on my computer (i5 processor) and installed gromacs 4.0.7. I have installed openmpi and fftw but when using mpirun command instead of getting parallel processes it simply runs the same job four times simultaneously. How do I make the necessary adjustments. Properly compile an MPI-enabled mdrun. Since you've provided no detail on how you did the installation, the only thing to suggest is that you've done something wrong. Follow the installation guide: http://www.gromacs.org/Downloads/Installation_Instructions Alternatively, use the newest version of Gromacs (4.5.3), which uses threading for parallelization instead of requiring external MPI support. -Justin Thanks, Gideon -- 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] g_lie query
Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Potential Energy = -nan
hi, I m tried nstxout=1 in my .mdp file. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! regards: shikha -- 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 query
Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values. I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run. -Justin Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] MPIRUN on Ubontu
In order to use MPI on Ubuntu with the distribution-supplied package, you need to use a combination of mpirun and mdrun_mpi, e.g. mpirun -np 2 mdrun_mpi -deffnm md to run on two cores. On Mon, Dec 27, 2010 at 7:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: גדעון לפידות wrote: Hi all, I have recently installed Ubonto on my computer (i5 processor) and installed gromacs 4.0.7. I have installed openmpi and fftw but when using mpirun command instead of getting parallel processes it simply runs the same job four times simultaneously. How do I make the necessary adjustments. Properly compile an MPI-enabled mdrun. Since you've provided no detail on how you did the installation, the only thing to suggest is that you've done something wrong. Follow the installation guide: http://www.gromacs.org/Downloads/Installation_Instructions Alternatively, use the newest version of Gromacs (4.5.3), which uses threading for parallelization instead of requiring external MPI support. -Justin Thanks, Gideon -- 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 list gmx-us...@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] Potential Energy = -nan
shikha agarwal wrote: hi, I m tried nstxout=1 in my .mdp file. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! The purpose of nstxout=1 is not to give you a different result. It might aid you in watching the trajectory to determine what is going wrong. From these values, and everything I have seen thus far, you have a physically unreasonable system. Either you have atomic overlap or a topology problem. Unless you provide substantially more diagnostic information, then pleas like help me will get you nowhere. You haven't even provided a description of your system beyond membrane protein. The contents, topology sources, steps taken up until now, etc are all necessary pieces of information. Please read the last sentence of the following page, and visit the link therein: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin regards: shikha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Potential Energy = -nan
hi, I tried on other system , 4GB ram , core i3 ,64bit processor ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) nstxout = 1 result Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=25000 Step= 14, Dmax= 1.2e-06 nm, Epot= -nan Fmax= 3.56233e+07, atom= 2455 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up after_em2.gro to ./#after_em2.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! shikha -- 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] glycam force field problem
Hi Xiaodu, Yes I remember now I had the same problem. Copy the forcefield.itp to your working directory and make the change there. Your working directory is searched first. However as you will be including a protein in your simulation you will need to have fudge set to 0.5 for 1-4 scaling with the AMBER forcefield... Personally I would look into doing mixed scaling with gromacs. This is how it is done in amber (the software package) when mixing these two forcefields but I can't help you here with gromacs, but I believe from reading the AMBER mailing list archive it is possible to scale on a per molecule basis. http://dev-archive.ambermd.org/200812/.html Here is the relevant part of the thread: Hi Rob, It was great to see you yesterday at the glycan array workshop. I'm here with Erik Lindahl, and we're chatting about implementing mixed 1-4 scaling in gromacs. It's easy to enable on a per-molecule basis. Enabling on a per-residue and per-atom basis is certainly possible, but there are a bunch of ways to do it. Do you have a sense of how you'd like to see this done? One idea would be to enable two different 1-4 pair types, one with default 1-4 scaling and one with user-specified scaling. And how should the interface be handled? I assume that it goes to default at that point (we want the protein 1-4 scaling at the NLN). Best wishes, --Peter 2010/12/27 gromacs564 gromacs...@126.com Hi Oliver I'm sorry to reply you so later.And I have some questions after reading your letter. You said that “The fudgeLJ under defaults should be 1.0 for GLYCAM“ and ”When you run grompp check in the output that fudge is set to 1.0.” Do you means to setting the fudgeLJ value to 1.0 in em.tpr file？I am not sure. I want to change this gromacs top files( all the output files by amb2gmx.pl converted) to gromacs itp files,then included in protein top file. And I plan to use the amber03 force filed. But I think that the [ defaults ] cannot included in itp files,or will cause an error about redifiniton.Because the [ defaults ] had exist in ”forcefield.itp. -- ;myt.itp [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5（ =1.0 ? ） 0.8333 #define _FF_AMBER #define _FF_AMBER03 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 -- So，do you know how to slove this problem？Can you give me some suggestion or a correct copy file by amb2gmx.pl converted? Thank you very much. My email address：gromacs...@126.com xiaodu -- 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] Potential Energy = -nan
shikha agarwal wrote: hi, I tried on other system , 4GB ram , core i3 ,64bit processor ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) nstxout = 1 result Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=25000 Step= 14, Dmax= 1.2e-06 nm, Epot= -nan Fmax= 3.56233e+07, atom= 2455 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up after_em2.gro to ./#after_em2.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! You've proven that the problem is not platform-specific, but you've provided none of the other details I requested before. Something is wrong with either the way you're building the system or constructed the topology. If you want free help, you have to make it easy to help you. So far, you haven't. Please consult my previous message and provide all the details I requested. Otherwise, you're unlikely to get anyone to help you. -Justin shikha -- 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] MPIRUN on Ubontu
I think you may need to type: module openmpi/gnu Then mpirun mdrun_mpi -v u know the rest Hassan On Dec 27, 2010, at 9:44 AM, גדעון לפידות glapid...@gmail.com wrote: Hi all, I have recently installed Ubonto on my computer (i5 processor) and installed gromacs 4.0.7. I have installed openmpi and fftw but when using mpirun command instead of getting parallel processes it simply runs the same job four times simultaneously. How do I make the necessary adjustments. Thanks, Gideon -- 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] minimization
Hi all, At the end of the minimisation I obtained potential energy value approximately -40,000 and I see the following warning Stepsize too small, or no change in energy.Converged to machine precision, but not to the requested precision Fmax 10 As far as I know for succesful minimisation potential energy must be between -100,000 and -1,000,000. My em.mdp file as follows integrator= steep emstep=0.1 nsteps=1000 nstlist=10 rlist=1.0 coulombtype=pme rcoulomb=1.0 vdw-type=cut-off rvdw=1.0 nstenergy=10 My minimisation stops at approximately 19,000 th step. Is my minimisation acceptable?If no, how can I correct it? best wishes Mustafa -- 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] minimization
mustafa bilsel wrote: Hi all, At the end of the minimisation I obtained potential energy value approximately -40,000 and I see the following warning Stepsize too small, or no change in energy.Converged to machine precision, but not to the requested precision Fmax 10 Please see the following: http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision As far as I know for succesful minimisation potential energy must be between -100,000 and -1,000,000. Potential energy is dependent upon system size and the nature of the interactions therein. You should not presuppose a specific value or range thereof. -Justin My em.mdp file as follows integrator= steep emstep=0.1 nsteps=1000 nstlist=10 rlist=1.0 coulombtype=pme rcoulomb=1.0 vdw-type=cut-off rvdw=1.0 nstenergy=10 My minimisation stops at approximately 19,000 th step. Is my minimisation acceptable?If no, how can I correct it? best wishes Mustafa -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MD simulation at 318K
Hi, I want to execute MD simulation of my Protein at 318K. Should I keep ref_t at 300K and gen_temp at 318K in the pr.mdp and md.mdp files? Do I need to change any other parameters as well. Thanks in advance, Regards, Swagata Chakraborty Research Scholar, Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai-45 -- 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] MD simulation at 318K
ref_t at 318K From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of swagata chakraborty [swagata.chakrabo...@gmail.com] Sent: Tuesday, December 28, 2010 3:17 PM To: gmx-users@gromacs.org Subject: [gmx-users] MD simulation at 318K Hi, I want to execute MD simulation of my Protein at 318K. Should I keep ref_t at 300K and gen_temp at 318K in the pr.mdp and md.mdp files? Do I need to change any other parameters as well. Thanks in advance, Regards, Swagata Chakraborty Research Scholar, Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai-45 CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- 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
