Re: [gmx-users] shall we use double precision?

Probably not. What does PLUMED documentation recommend? Mark On Jun 11, 2013 7:36 AM, "Albert" wrote: > Hello : > > I am going to use Gromacs with PLUMD plugin to perform Metadynamics. > Since this methods involved in free energy calculations, I am just > wondering is it necessary to introduce

Re: [gmx-users] restraints on water oxygen atoms

These are the all commands to do iteration: After generating topology -    concatenate the protein and bilayer structure files:     #cat dimer-newbox.gro popc-whole.gro > system.gro   ( Remove unnecessary lines and update the second line of the coordinate file (total number of atoms) ac

[gmx-users] shall we use double precision?

Hello : I am going to use Gromacs with PLUMD plugin to perform Metadynamics. Since this methods involved in free energy calculations, I am just wondering is it necessary to introduce double precision Gromacs? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] A charge group moved too far between two domain decomposition steps

Dear Gromacs users, I tried to do the simulation of a single molecule in cyclohexane, I'm using gromos 53a6 force field for both molecules. i did all the minimization steps. After npt, I runned for 25 000 000 steps. just after around 100 000 steps, the system stops and i got this fatal error: Fa

RE: [gmx-users] Re: Unable to download Gromacs source tar file

-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Christoph Junghans Sent: Sat 6/8/2013 10:40 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: Unable to download Gromacs source tar file > Date: Sat, 8 Jun 2013 13:57:51 +0200 > From: Mark Abraham > Subject: Re: [

[gmx-users] stay at some temperature during annealing

Hi guys, I am using simulated annealing for my protein+water+Ion system, I tried to let the system stay at some temperature for a while, e.g.: stay at 600k from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is like: annealing_time = 0 3000 1 2 0 3000 1 2 0 300

Re: [gmx-users] Error in grompp minimization

Dear Justin, thank you for your reply. Yes, you are right , I have corrected it already and now it works well. Cheers, Safa On 11 June 2013 09:53, Justin Lemkul wrote: > > > On 6/10/13 8:51 PM, Souilem Safa wrote: > >> Dear gromacs users, >> >> I'm trying to simulate a single molecule in cycloh

Re: [gmx-users] Error in grompp minimization

On 6/10/13 8:51 PM, Souilem Safa wrote: Dear gromacs users, I'm trying to simulate a single molecule in cyclohexane. I made a box of my molecule using editconf command and next I solvate with cyclohexane using genbox command : genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro

[gmx-users] Error in grompp minimization

Dear gromacs users, I'm trying to simulate a single molecule in cyclohexane. I made a box of my molecule using editconf command and next I solvate with cyclohexane using genbox command : genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro I did next a position restraint in the top

Re: [gmx-users] Re: Free Energy Calculations in Gromacs

An important final point is that you can always see EXACTLY what grompp is putting into the B state by running gmxdump on the resulting tpr. It's a LOT of information, but all in text all the interactions are listed explicitly there. On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul wrote: > > > On

Re: [gmx-users] Re: Genbox center of box

On 6/10/13 3:26 PM, Matt Bawn wrote: I have never seen such a prompt, and I cannot reproduce the problem with version 4.5.5 on my machine. Did you install from source, or from some external binary or package manager? Are you running Gromacs directly, or are you using any GUI interface o

Re: [gmx-users] Re: Free Energy Calculations in Gromacs

On 6/10/13 2:50 PM, JW Gibbs wrote: Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefi

[gmx-users] gromacs 4.6.2 MPI distribution location problems

Hi All, I installed gromacs 4.6.2 using the following cmake options: cmake -DCMAKE_INSTALL_PREFIX=/home/kaushik/gromacs_executable/gromacs-new-mpi -DGMX_MPI=on After successful installation, when I run a test with mpirun mdrun, the program breaks with the following error: ---

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Szilárd, I tried the build using a PATH without the Intel compilers and NOT including the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it used the FFTW 3.2 wrappers to MKL. Here is the output from mdrun -version: Program: mdrun Gromacs version:VERSION 4.6.1 Precisi

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Szilárd, I just tried the cmake with -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and got a successful build. When I ran the regression tests I got the following results (grepped out the summary lines): All 16 simple tests PASSED All 19 complex tests PASSED All 142 kernel tests PASSED

[gmx-users] Re: Genbox center of box

>I have never seen such a prompt, and I cannot reproduce the problem with version >4.5.5 on my machine. Did you install from source, or from some external binary >or package manager? Are you running Gromacs directly, or are you using any GUI >interface of any sort? Does the problem persist with

[gmx-users] Re: Free Energy Calculations in Gromacs

Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happe

Re: [gmx-users] Re: Genbox center of box

On 6/10/13 2:33 PM, Matt Bawn wrote: Can you please provide your exact sequence of commands (up to, and including, genbox) and the exact error message (copied and pasted from the terminal)? Which version of Gromacs are you using? I'm using Gromacs 4.5.5 1 pdb2gmx -f 2CCA_dw.pdb -o 2CCA_p

Re: [gmx-users] restraints on water oxygen atoms

On 6/10/13 12:24 PM, Shima Arasteh wrote: Would you please tell me which initial deletion radius? It would be easier for you to provide the exact command(s) you're using. Maybe you've posted this information before, but this thread (or at least, related topics) has gone on for a very long

[gmx-users] Re: Genbox center of box

>Can you please provide your exact sequence of commands (up to, and including, >genbox) and the exact error message (copied and pasted from the terminal)? >Which version of Gromacs are you using? I'm using Gromacs 4.5.5 1 pdb2gmx -f 2CCA_dw.pdb -o 2CCA_processed.gro -water spce -merge all FF

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

On Mon, Jun 10, 2013 at 6:11 PM, Szilárd Páll wrote: > Amil, > > It looks like there is a mixup in your software configuration and > mdrun is linked against libguide.so, the OpenMP library part of the > Intel compiler v11 which gets loaded early and is probably causing the > crash. This library wa

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

On Mon, Jun 10, 2013 at 4:57 PM, Amil Anderson wrote: > Roland, > > Here is the output from the debug run with the stack trace: > > [aanderson@warp2-login gmxdemo]$ gdb mdrun > GNU gdb Fedora (6.8-27.el5) > Copyright (C) 2008 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or la

Re: [gmx-users] restraints on water oxygen atoms

Would you please tell me which initial deletion radius? And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly?   Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Monday,

Re: [gmx-users] Genbox center of box

On 6/10/13 12:13 PM, Matt Bawn wrote: I am beginning a simulation of my system following the lysozyme tutorial but when I try to use genbox to solvate my system it asks me to provide the coordinates of the center of the box. I have previously been successfully able to enter the same commands wi

[gmx-users] Genbox center of box

I am beginning a simulation of my system following the lysozyme tutorial but when I try to use genbox to solvate my system it asks me to provide the coordinates of the center of the box. I have previously been successfully able to enter the same commands without this prompt appearing from gromacs.

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Amil, It looks like there is a mixup in your software configuration and mdrun is linked against libguide.so, the OpenMP library part of the Intel compiler v11 which gets loaded early and is probably causing the crash. This library was probably pulled in implicitly by MKL which the build system det

Re: [gmx-users] restraints on water oxygen atoms

On 6/10/13 11:44 AM, Shima Arasteh wrote: Thanks for your reply. When I look into the earlier gro file ( with APL even higher than 10% of desired APL), I still see some lipid residues in improper places, forexample in phenyl rings. How can I go on with it? If I choose the gro file without any

Re: [gmx-users] restraints on water oxygen atoms

Thanks for your reply. When I look into the earlier gro file ( with APL even higher than 10% of desired APL), I still see some lipid residues in improper places, forexample in phenyl rings. How can I go on with it? If I choose the gro file without any overlap, the APL becomes very high and it wo

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Roland, Here is the output from the debug run with the stack trace: [aanderson@warp2-login gmxdemo]$ gdb mdrun GNU gdb Fedora (6.8-27.el5) Copyright (C) 2008 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are

Re: [gmx-users] Seeing Martini membrane trajectory files

On 6/10/13 10:07 AM, Neha wrote: Hi everybody! I have a quick question about VMD and trajectory files. It seems that VMD should be able to be use to view Gromacs trajectory files. I am working with lipid membranes, and I was able to view the final .gro file with VMD. However I was not able to

[gmx-users] Seeing Martini membrane trajectory files

Hi everybody! I have a quick question about VMD and trajectory files. It seems that VMD should be able to be use to view Gromacs trajectory files. I am working with lipid membranes, and I was able to view the final .gro file with VMD. However I was not able to see the entire trajectory, and I am n

Re: [gmx-users] Angles not read

On Mon, Jun 10, 2013 at 2:24 PM, Justin Lemkul wrote: > > > On 6/10/13 9:22 AM, Steven Neumann wrote: > >> On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/10/13 9:11 AM, Steven Neumann wrote: >>> >>> Thank you Justing. Last question - each of my amino acid is one bead.

Re: [gmx-users] Angles not read

On 6/10/13 9:22 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul wrote: On 6/10/13 9:11 AM, Steven Neumann wrote: Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? S

Re: [gmx-users] Angles not read

On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul wrote: > > > On 6/10/13 9:11 AM, Steven Neumann wrote: > >> Thank you Justing. Last question - each of my amino acid is one bead. How >> can I specify [angles ] between atoms corresponding to different residues? >> Shall I add it at the end of my rtp

Re: [gmx-users] Angles not read

On 6/10/13 9:11 AM, Steven Neumann wrote: Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? Shall I add it at the end of my rtp entry with all amino acids? Each .rtp entry should only contain o

Re: [gmx-users] Angles not read

Thank you Justing. Last question - each of my amino acid is one bead. How can I specify [angles ] between atoms corresponding to different residues? Shall I add it at the end of my rtp entry with all amino acids? On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul wrote: > > > On 6/10/13 9:04 AM, St

Re: [gmx-users] Angles not read

On 6/10/13 9:04 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul wrote: On 6/10/13 8:53 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: O

Re: [gmx-users] Angles not read

On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul wrote: > > > On 6/10/13 8:53 AM, Steven Neumann wrote: > >> On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/10/13 8:42 AM, Justin Lemkul wrote: >>> >>> On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, J

Re: [gmx-users] Angles not read

On 6/10/13 8:53 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote: On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: D

Re: [gmx-users] Angles not read

On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote: > > > On 6/10/13 8:42 AM, Justin Lemkul wrote: > >> >> >> On 6/10/13 8:40 AM, Steven Neumann wrote: >> >>> On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote: >>> >>> On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx U

Re: [gmx-users] Angles not read

On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is p

Re: [gmx-users] Angles not read

On 6/10/13 8:42 AM, Justin Lemkul wrote: On 6/10/13 8:40 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote: On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads

Re: [gmx-users] Angles not read

On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote: > > > On 6/10/13 8:23 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> I created my own CG force field and i process my structure to pdb2gmx. I >> process 3 beads I created to check whether the topology is properly >> created: >> >> >> Usi

Re: [gmx-users] Angles not read

On 6/10/13 8:23 AM, Steven Neumann wrote: Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will

[gmx-users] Angles not read

Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created: Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_C

Re: [gmx-users] restraints on water oxygen atoms

On 6/10/13 3:37 AM, Shima Arasteh wrote: Thanks for your reply. The system I am trying to equilibrate is composed of popc/ peptide/ions/water. I built the system by InflateGRO methodology as you wrote in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, was used as the

Re: [gmx-users] Quartic angle potential - how to use?

On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Nothing in the manual seems to suggest that such a form is supported. -Justin

[gmx-users] site-site Coulombic force

Hi all,  Is it possible in GROMACS to print  the individual site-site Coulombic force along with respective co-ordinates of the sites in each time step as output e.g. for simulation of rigid water.  Thanks,  Best regards  Biki -- View this message in context: http://gromacs.5086.x6.nabble.

Re: [gmx-users] Quartic angle potential - how to use?

Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Steven On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul wrote: > > > On 6/5/13 8:40 AM, Steven Neumann wrote: > >> Dear Gmx Us

Re: [gmx-users] restraints on water oxygen atoms

Thanks for your reply.   The system I am trying to equilibrate is composed of popc/ peptide/ions/water. I built the system by InflateGRO methodology as you wrote in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, was used as the starting configuration in next steps. But b

Re: [gmx-users] Eigenvector and eigenvalues

Hi Ankitha, Taking the backbone for analysis doesn't give you more information than using only C-alphas. These are extremely correlated. Cheers, Tsjerk On Sun, Jun 9, 2013 at 5:28 PM, Ankita naithani wrote: > Hi Tsjerk, > > Thank you so much for the helpful insight. It will surely help in cl