[gmx-users] grompp error
Hi I am using gromacs 4.5.3 ... I am using OPLSS force field in simulation and while issuing grompp command for energy minimzation I am getting an error "No molecule type NA+ exists" ... I used NA+ while issuing genion command ..., can anybody tell me where am I going wrong?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.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] segmentation error
I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and temperature. before reducing temperature is 300 and after reducing it is 2.5) -- 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] Installing Gromacs with Cygwin
Dear all, I need help. I am trying to install Gromacs using Cygwin. However, I do not seem to have access to it. I am very new with Cygwin. I just followed the steps provided by the following sites: http://machine-phase.blogspot.com/2009/04/how-to-install-gromacs-on-windows-vista.html and http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO but in the end when I type "luck" it returns "command not found". These are the steps I did. 1. Downloaded fftw-3.2.2 and gromacs-4.5.3 and saved them in C:\Packages 2. After installing cygwin, I changed directory by typing in the following in order to work with fftw-3.2.2 cd /cygdrive/c/Packages/fftw-3.2.2 and then I typed in ./configure --enable-threads --enable-sse w--enable-float followed by make then make install 2. I then worked for the gromacs-4.5.3 by typing in cd /cygdrive/c/Packages/gromacs-4.5.3 and then ./configure --enable-shared LDFLAGS="-L/usr/local/lib" make make install make links make clean 3. I typed "luck" after all the procedures above but what I get is "command not found". I am still at /cygdrivec/Packages/gromacs-4.5.3. Is this the correct path to run the gromacs? Please help. 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
Re: [gmx-users] Installing Gromacs with Cygwin
On 16/01/2011 9:27 PM, Mr Bernard Ramos wrote: Dear all, I need help. I am trying to install Gromacs using Cygwin. However, I do not seem to have access to it. I am very new with Cygwin. I just followed the steps provided by the following sites: http://machine-phase.blogspot.com/2009/04/how-to-install-gromacs-on-windows-vista.html and http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO but in the end when I type "luck" it returns "command not found". These are the steps I did. 1. Downloaded fftw-3.2.2 and gromacs-4.5.3 and saved them in C:\Packages 2. After installing cygwin, I changed directory by typing in the following in order to work with fftw-3.2.2 cd /cygdrive/c/Packages/fftw-3.2.2 and then I typed in ./configure --enable-threads --enable-sse w--enable-float Hopefully that extra 'w' is spurious. Actually copying and pasting is a good practice. followed by make then make install 2. I then worked for the gromacs-4.5.3 by typing in cd /cygdrive/c/Packages/gromacs-4.5.3 and then ./configure --enable-shared LDFLAGS="-L/usr/local/lib" make make install make links make clean 3. I typed "luck" after all the procedures above but what I get is "command not found". I am still at /cygdrivec/Packages/gromacs-4.5.3. Is this the correct path to run the gromacs? See the official installation instructions regarding getting access to GROMACS after installation. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation error
On 16/01/2011 8:43 PM, leila separdar wrote: I managed to run my simulation but which kind of coulomtype can I use except PME? Do you have charges? If so, follow standard practice in the literature for treating them. also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and temperature. before reducing temperature is 300 and after reducing it is 2.5) Write out the equations in a form such that the values you must input into GROMACS can be clearly identified. Anything else is a recipe for trouble, unless you're following published literature. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp error
On 16/01/2011 7:09 PM, bharat gupta wrote: Hi I am using gromacs 4.5.3 ... I am using OPLSS force field in simulation and while issuing grompp command for energy minimzation I am getting an error "No molecule type NA+ exists" ... I used NA+ while issuing genion command ..., can anybody tell me where am I going wrong?? Different force fields use different names for species. Look up $GMXLIB/oplsaa.ff/ions.itp to see how the molecules, residues and atoms should be named. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with LINCS
Hello! I have the following problem: I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equilibration. A few steps after the volume equilibration, I got this message: Step 2160, time 4.32 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2702.127453, max 65115.246094 (between atoms 130 and 131) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 121123 91.90.1378 0.6015 0.1378 130131 90.00.1526 9936.7393 0.1526 ... I use LINCS with h-angles. The whole procedure works when I don't use the conformer pair, but two separate ions inserting randomly in the box. I get no LINCS warning. What can be the problem? Regards and thanks, Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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] problem with LINCS
Thomas Koller wrote: Hello! I have the following problem: I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equilibration. A few steps after the volume equilibration, I got this message: Step 2160, time 4.32 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2702.127453, max 65115.246094 (between atoms 130 and 131) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 121123 91.90.1378 0.6015 0.1378 130131 90.00.1526 9936.7393 0.1526 ... I use LINCS with h-angles. The whole procedure works when I don't use the conformer pair, but two separate ions inserting randomly in the box. I get no LINCS warning. What can be the problem? Hard to say. What does the trajectory show? How successful was energy minimization, and what were your criteria? What's in your .mdp file? Additional troubleshooting points can be found here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin Regards and thanks, Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ACPYPE download
Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone who has successful experience using ACPYPE and would be willing to provide me the program? Thanks a lot. JH -- 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] Position restraint problem
Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tried to restrain the positions of the perfluorohexane molecules using -DPOSRES (I've attached the mdp file). The problem is that mdrun keeps running in background but there's no output showing in the sa.log file. What could be the problem? Thank you. sa.mdp Description: application/mdp -- 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] Position restraint problem
Marcelo Silva wrote: Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tried to restrain the positions of the perfluorohexane molecules using -DPOSRES (I've attached the mdp file). The problem is that mdrun keeps running in background but there's no output showing in the sa.log file. What could be the problem? Are other files being written to? If not, the run probably crashed. All output is buffered, so it may just take time to show up. If you want to try to debug, set the LOG_BUFS environment variable to 0. The resulting run will be unbuffered and very slow, however. -Justin Thank you. -- 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] Position restraint problem
On 17/01/2011 6:25 AM, Marcelo Silva wrote: Hello everybody, I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration. Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tried to restrain the positions of the perfluorohexane molecules using -DPOSRES (I've attached the mdp file). Sounds like you might need to check out FAQ #11. http://www.gromacs.org/Documentation/FAQs The problem is that mdrun keeps running in background but there's no output showing in the sa.log file. What could be the problem? File systems store I/O in temporary areas in memory, and only write periodically. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ACPYPE download
On 17/01/2011 5:05 AM, Jianhui Tian wrote: Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone who has successful experience using ACPYPE and would be willing to provide me the program? Did you find this page? http://code.google.com/p/acpype/wiki/HowToUse Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ACPYPE
Go to http://code.google.com/p/acpype/wiki/HowToUse for instructions on installation of ACPYPE. There are also some very nice acpype tutorials located at http://code.google.com/p/acpype/w/list Enjoy! John John E. Kerrigan, Ph.D. Associate Director Bioinformatics The Cancer Institute of New Jersey 120 Albany Street New Brunswick, NJ 08903 Phone: 732 235-4473 Fax: 732 235-6267-- 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] Viscosity calculations
Hi, I'm trying to calculate viscosities of a few ionic liquid and has roughly read about Hess's paper JCP 116 209, 2002. Follows are the questions that I have (1) For the method which uses the fluctuations of the pressure tensor using Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis option and has obtained a few files such as evisco.xvg, eviscoi.xvg and visco.xvg The evisco.xvg seems like the one I'm interested, since it has the title as @title "Shear viscosity using Einstein relation" and the unit seems also correct. This file has 5 columns, if I understand it correctly(by extrapolating from Hess's paper), the second to fourth columns are the results from the off-diagonal elements of the pressure tensor and the fifth one being the average. Hess's paper seems to be this one(Figure 5). However, the results are way to low for the ionic liquid, since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid. the eviscoi.xvg file seems to be some kind of integral of evisco.xvg which I'm not quite getting what it is. visco.xvg contains the shear viscosity and bulk viscosity, which again seems to be the one I'm looking for. However, the shear viscosity I'm looking is(the region which roughly is constant) about 3~5 times higher than the experiment. The simulation is 12ns long. Of course, this could mean (1) the force field is bad or (2) the Green-kudo converges too slowly as Hess pointed out. Since it is not getting any useful result, I turned to non-equilibrium MD by applying a shear external force, which is in (2) (2) I tried both NVT and NPT simulations which uses berendsen coupling bath. and set up the cos_acceleration = 0.1 nm/ps^2. However, I tried to use g_energy -f *edr -s *tpr and by selecting the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero data points on all times. I tried really hard on searching results on the user list of gromacs but it seems that there are quite a lot questions on this but not a single satisfactory answer has been given, the most popular answer people gave is refer to Hess's paper, but even though Hess was giving a good theoretical background on this paper, practically on how to set up MD jobs is not given. So I would appreciate anyone's hint. Cheers, Xiaohu -- 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
