[gmx-users] Updating Ubuntu

Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does anyone know or have the possibility to update UBUNTU with the latest GMX? Cheers Sergio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] reading tpx file version 73 with version 58 program

you have generated your em1.tpr file using a newer gromacs version, and are trying to read it with an older gromacs version. Please make sure you use the same gromacs version. Try typing which grompp to find out. On Fri, Dec 24, 2010 at 8:49 AM, shikha agarwal shikhaiiit...@gmail.comwrote: hi

Re: [gmx-users] reading tpx file version 73 with version 58 program

On 24/12/2010 6:49 PM, shikha agarwal wrote: hi , Mr. justin thanx a lot for ur help! now i m able to generate system_inflated.gro. but while i m performing Run energy minimization accorning to tutorial getting this error grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr mdrun

Re: [gmx-users] Installation GROMACS UBUNTU

On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46

Re: [gmx-users] Updating Ubuntu

On 24/12/2010 8:20 PM, Sergio Manzetti wrote: Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does anyone know or have the possibility to update UBUNTU with the latest GMX? If it's not in the package manager, than whoever contributed it to Ubuntu hasn't updated it, I'm

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica

[gmx-users] Reg: Simulating large number of molecules

Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system after running some time it says cannot allocate memory but when

Re: [gmx-users] Reg: Simulating large number of molecules

On 2010-12-24 11.06, vinothkumar mohanakrishnan wrote: Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system after

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong

Re: Re: [gmx-users] mdrun mpi segmentation fault in high load situation

I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing what condition led to the problem. Mark

[gmx-users] nve simulation

Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.can anyone help me out with this. regards, sree. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Installation GROMACS UBUNTU

Not really, there were no errors with ./configure so I downloaded the version through ubunto sudo -apt get install gromacs but it was old version On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 2010-12-24 13.15, ms wrote: On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope

Re: [gmx-users] mdrun mpi segmentation fault in high load situation

On 24/12/2010 9:59 PM, Wojtyczka, André wrote: I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing

Re: [gmx-users] Reg: Simulating large number of molecules

On 24/12/2010 9:06 PM, vinothkumar mohanakrishnan wrote: Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system

Re: [gmx-users] amber convert gromacs input files

Have a good look in acpype, specially its wiki. There you'll see that acpype is totally new code and among other things it covers amb2gmx.pl and solves several of its drawbacks. It's not perfect though but for a system created in tleap, the project is likely to be completed converted to gmx. Alan

Re: [gmx-users] Installation GROMACS UBUNTU

Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Not really, there were no errors with ./configure That's simply not possible. The purpose of configuration is to determine specifications of your system, which are then used to write the Makefile. If you have no Makefile, then something

Re: [gmx-users] Installation GROMACS UBUNTU

Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is

Re: [gmx-users] Installation GROMACS UBUNTU

Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install...

Re: [gmx-users] Installation GROMACS UBUNTU

Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul

Re: [gmx-users] Installation GROMACS UBUNTU

Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not.

Re: [gmx-users] Installation GROMACS UBUNTU

Thanks again J, is that compulsory each time one installs something new? On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks J, I think I will install Ubuntu entirely first, because I just tried to install

Re: [gmx-users] Installation GROMACS UBUNTU

Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove

Re: [gmx-users] Installation GROMACS UBUNTU

Justin, THe FFTW messagte was AFTER sudo make install. On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove

Re: [gmx-users] Installation GROMACS UBUNTU

Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Justin, THe FFTW messagte was AFTER sudo make install. Then you're not an admin. You can always do the installations in your home directory (for both FFTW and Gromacs) by specifying an appropriate --prefix during configuration. -Justin

Re: [gmx-users] Installation GROMACS UBUNTU

Thanks, but I will start from scratch. On Fri, Dec 24, 2010 at 3:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Justin, THe FFTW messagte was AFTER sudo make install. Then you're not an admin. You can always do the installations

[gmx-users] simulation at constant temprature

Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.I am usng leap frog as integrator .can anyone help me out with this.how to do the velocity rescaling regards, sree. --

[gmx-users] number of coordinates in coordinate file does not match topology

hello I m unable to update the [ molecules ] directive of topol_pope.top . grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr Fatal error: number of coordinates in coordinate file (system_inflated.gro, 20782) does not match topology (topol_pope.top, 37867)

Re: [gmx-users] simulation at constant temprature

On Fri, 24 Dec 2010 06:36:03 -0800 sreelakshmi ramesh sree.laks...@research.iiit.ac.in wrote: Dear Gmx users, I wanted to do a simulation with NVE ensemble but i want the temprature to be always around 300k but in my simulation the temp is 380k.I am usng leap frog as

Re: [gmx-users] number of coordinates in coordinate file does not match topology

Quoting shikha agarwal shikhaiiit...@gmail.com: hello I m unable to update the [ molecules ] directive of topol_pope.top . grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr Fatal error: number of coordinates in coordinate file (system_inflated.gro, 20782)

[gmx-users] velocity rescaling

what is velocity rescaling and how to use it in nve simulations. 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

Re: [gmx-users] velocity rescaling

Quoting sreelakshmi ramesh sree.laks...@research.iiit.ac.in: what is velocity rescaling and how to use it in nve simulations. Velocity rescaling is a method for controlling temperature by modifying the kinetic energy. In an NVE simulation, thermostats are not used. -Justin thanks in

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the

Re: [gmx-users] dssp

mustafa bilsel wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv

[gmx-users] minimization

Dear Justin, I have added your last reply to the end of this message. my shell type is bash. my dssp exe file is in /home/m/DSSP/dssp I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did do_dssp I have the below error. Although the dssp exe is in /usr/local/bin and also I did

[gmx-users] minimization

Hi, What is the meaning of the below message after I completed minimization? Does it mean minimization is successful? In my input parameters nsteps=10,000,000 but minimization stops at about 14,000 th step. Is 10,000,000 very large? What is the typical value for it? And also what is the meaning

Re: [gmx-users] minimization

mustafa bilsel wrote: Dear Justin, I have added your last reply to the end of this message. my shell type is bash. my dssp exe file is in /home/m/DSSP/dssp I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did This is still wrong. As I quoted in the previous message, the

Re: [gmx-users] minimization

mustafa bilsel wrote: Hi, What is the meaning of the below message after I completed minimization? Does it mean minimization is successful? In my input parameters nsteps=10,000,000 but minimization stops at about 14,000 th step. Is 10,000,000 very large? What is the typical value for it?

Re: [gmx-users] Nose-hoover T-coupling in REMD

Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the

[gmx-users] generate .top file

hello Merry Christmas. this is my topol_pope.top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ;

[gmx-users] pulling

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