Re: [gmx-users] Removing Water from Final Simulation

... and see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volumefor prevention cure. Mark On Mon, Jun 3, 2013 at 3:47 AM, Dallas Warren dallas.war...@monash.eduwrote: trjconv for trajectories editconf for coordinate files Along with an appropriately generated

Re: [gmx-users] About the binary identical results by restarting from the checkpoint file

On Sun, Jun 2, 2013 at 10:37 PM, Cuiying Jian cuiying_j...@hotmail.comwrote: Hi GROMACS Users, These days, I am testing restarting simulaitions with .cpt files. I already set nlist=1 in the .mdp file. I can restart my simulations (which are stopped manually) with the following commands

Re: [gmx-users] Pressure coupling

Probably. See manual 7.3.15. Semiisotropic with some zero compressibilities is probably what you want. Mark On Sun, Jun 2, 2013 at 9:33 PM, Marcelo Vanean vanea...@gmail.com wrote: Hello everyone. I want to know if can be applied pressure coupling only in the z direction, allowing the edges

Re: [gmx-users] fattyn acid parameter in OPLSAA forcefield

Please email just gmx-users, not the owner or request addresses :-) On Sun, Jun 2, 2013 at 9:37 PM, fatemeh ramezani fr_...@yahoo.com wrote: Hi all I want to simulate protein-fatty acid-AU complexs by OPLSAA force field. But OPLSAA force field, hasn't any parameter for fatty acid. Can I

[gmx-users] Re: umbrella sampling for two polymer interaction

Sorry, my writing was not really excat. If you use a reference group, the force / potential acting on the pulled group is always relative to the reference group. If you use 'pull_geometry = distance' the origin potential is always in the distance 'pull_init1' along the vector from the reference

Re: [gmx-users] structure alignement :g_rmsdist

Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond to the frame at time 0?? Because in the manual the rmsd equation show that reference structure correspond to the time t=0 but the help doesn't confirm. THanks a lot for your help, 2013/6/2 Tsjerk

Re: [gmx-users] structure alignement :g_rmsdist

Hi Nawel, The reference distances are computed from the reference structure provided with the option -s. Cheers, Tsjerk On Mon, Jun 3, 2013 at 12:39 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond

Re: [gmx-users] structure alignement :g_rmsdist

Thanks, the tpr file using by -s option contains the starting structure of the simulation so the reference structure correspond to the first structure. Thanks a lot , 2013/6/3 Tsjerk Wassenaar tsje...@gmail.com Hi Nawel, The reference distances are computed from the reference structure

Re: [gmx-users] Vritual Sites and simulation time-step

Mark, I've performed 50 ns simulation of water-soluble protein with and without VS. As the consequence I've observed similar behavior of both systems in case of secondfary structure conservation as well as overal degree of conformational dynamics. Also I didnt observed any fluctuation in energy

[gmx-users] gmx 4.6.2 segementation fault (core dump)

Hi there, trying to set up gmx-4.6.2, compiled with cuda 5.0.35 and gcc 4.7.2 on fedora linux, but it only gives me a segementation fault (core dump) on mdrun startup. Same compiling options on gmx 4.6.1 gives me a running mdrun. Did anyone encounter the same problem? Thanks, Johannes --

[gmx-users] How to compile/run Gromacs on native Infiniband?

Dear all, My cluster has a FDR (56 Gb/s) Infiniband network. It is well known that there is a big difference between using IPoIB (IP over IB) with a normal sockets application and using native InfiniBand with an application that has been coded directly to the native IB verbs interface. The latter

[gmx-users] CG angle distribution

Dear Gmx Users, I am building coarse-grained model for my protein. I group them int0 5-10 atoms. I wish to reproduce atomistic equilibrium angles as well as the spring constant. Shall I use g_angle -od option and calulate distributions? Then I will use equilibrium th0 as the centre of the

[gmx-users] frame

Hi, if I run 20ns MD, and want to get the pdb at 19532ps trjconv -s md_0_1.tpr -f md_0_1.xtc -o bovin19532.gro -dt 1 -b 19532 -e 19532 editconf -f bovin19532.gro -o bovin19532.pdb If is it right? Thank you very much! -- View this message in context:

Re: [gmx-users] frame

better to convert ur frames in a time (ps) and use trjconv -dump to write out the frame. -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475

[gmx-users] using previous window restart file

Dear All, (Sorry for long mail!) (Thanks Thomas Schlesier for clarifying previous umbrella queries) I wish to run umbrella samplings using restart file of previous window. e.g. initial distance between A (reference) and B (pulled group) is 1 nm (10 Angs) then I intend to run 10 windows after

[gmx-users] Re: gmx 4.6 mpi installation through openmpi?

Hello all, I have a very similar problem, but compiling both Gromacs 4.6 and 4.6.1 with cmake and MPI support (no problems with non-MPI installation). I have cmake version 2.8.7, openmpi version 1.4.1, and I am using gcc version 4.6.3 in a linux Ubuntu 4.6.3. I use the cmake options: cmake

Re: [gmx-users] gmx 4.6.2 segementation fault (core dump)

Thanks for reporting this. he best would be a redmine bug with a tpr, command line invocation for reproduction as well log output to see what software and hardware configuration are you using. Cheers, -- Szilárd On Mon, Jun 3, 2013 at 2:46 PM, Johannes Wagner johannes.wag...@h-its.org wrote:

Re: [gmx-users] gmx 4.6.2 segementation fault (core dump)

hi, thanks for the prompt replies ~/programs/gromacs-4.6.2/bin$ ./mdrun -version Program: ./mdrun Gromacs version:VERSION 4.6.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:

Re: [gmx-users] gmx 4.6.2 segementation fault (core dump)

I can't reproduce it on a very similar hardware and software configuration. Can you provide a tpr? Is the segfault reproducible with multiple configurations? Does mdrun work without GPUs (-nb cpu or GMX_DISABLE_GPU_DETECTION=1 env. var)? -- Szilárd On Mon, Jun 3, 2013 at 4:12 PM, Johannes Wagner

[gmx-users] Setting total simulation time

Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would these be the correct input parameters? Thanks! ; Run parameters integrator = md nsteps = 50 dt = 0.002 ; Output control nstxout = 1000 nstvout = 1000 nstenergy

[gmx-users] Re: frame

How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: gmx 4.6 mpi installation through openmpi?

That looks like there's a PGI compiler getting used at some point (perhaps the internal FFTW build is picking up the CC environment var? I forget how that gets its compiler!). If you do find * -name config.log then perhaps you can see in that file what the FFTW build thinks about its compiler.

Re: [gmx-users] Setting total simulation time

Try smaller numbers and periods for a test run, and see the machinery work. gmxcheck on the output files is your friend! Mark On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal parker.dewaa...@kzoo.eduwrote: Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would

Re: [gmx-users] Re: frame

You chose your time step... ;-) Mark On Mon, Jun 3, 2013 at 4:50 PM, maggin maggin.c...@gmail.com wrote: How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the

Re: [gmx-users] Re: frame

well, you basically just did it… 20ns is 20,000ps. so trjconv -dump 19532 -s xxx -f xxx -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475

[gmx-users] frame in VMD

Hi, I use VMD to see GROMACS trajectory, I run 20ns md, there are 10,000,000 step, when load to VMD, it total 2777 frames. I don't known if there something wrong in it ? How to get the frame about 19532ps? Thank you very much! maggin -- View this message in context:

Re: [gmx-users] frame in VMD

Probably, VMD tries to load the whole trajectory into memory, and that runs out. You should be using trjconv to get a particular frame. Also see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume to avoid generating redundant information to throw away later. Mark On

Re: [gmx-users] Vritual Sites and simulation time-step

Hi James, Not related to the integration stability as such, but since the vsites affect the hydrogens by definition perhaps g_hbond can reveal systematic differences between simulations with and without vsites. I believe Feenstra et al did this in the paper describing vsites in the first

[gmx-users] Creating a monolayer from Martini bilayer

Hello everybody, I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For periodic boundary

Re: [gmx-users] Setting total simulation time

Thanks Mark, Using the above I ran gmxcheck -f nvt.trr Here is the resulting out put Last frame500 time 1000.000 Item#frames Timestep (ps) Step 5012 Time 5012 Lambda 5012 Coords 5012 Velocities 5012 Forces 0

Re: [gmx-users] Creating a monolayer from Martini bilayer

You could try packmol or the MembraneEditor. http://www.cellmicrocosmos.org/index_cm2.php Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 03.06.2013 um 18:43 schrieb Neha nshafi...@wesleyan.edu: Hello everybody, I am a new user to Gromacs and am working on lipid simulations

Re: [gmx-users] Creating a monolayer from Martini bilayer

Hey :) Just center the bilayer around z=0, solvate and put all molecules in the box with trjconv. Then add 10 to the PBC Z-component (third number from the last line in the .gro file). Cheers, Tsjerk On Mon, Jun 3, 2013 at 6:55 PM, Gunther Lukat g.lu...@gmx.net wrote: You could try packmol

[gmx-users] RE: About the binary identical results by restarting from the checkpoint file

Hi Mark, Thanks for your reply. I tested restarting simulations with .cpt files by GROMACS 4.6.1. and the problems are still there, i.e. I cannot get binary identical results from restarted simulations with those from continuous simulations. The command I used for restarting is as the

Re: [gmx-users] Creating a monolayer from Martini bilayer

On 03.06.2013 18:43, Neha wrote: I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For

Re: [gmx-users] RE: About the binary identical results by restarting from the checkpoint file

On Mon, Jun 3, 2013 at 6:59 PM, Cuiying Jian cuiying_j...@hotmail.comwrote: Hi Mark, Thanks for your reply. I tested restarting simulations with .cpt files by GROMACS 4.6.1. and the problems are still there, i.e. I cannot get binary identical results from restarted simulations with those

[gmx-users] Re: Creating a monolayer from Martini bilayer

Hi, thank you so much! This way seems promising, however I am not sure how to center the bilayer around z=0. I thought I could use editconf but I might be confused as to how Gromacs centers its objects. If I put -center 0 0 0 does that mean the bilayer is centered around z = 0? Also I thought

Re: [gmx-users] Re: Creating a monolayer from Martini bilayer

Hi Neha, A single structure is like a trajectory with only one frame :p trjconv works on those as well. Right, set the center at 0,0,0 and choose the lipids as group for centering. Cheers, Tsjerk On Mon, Jun 3, 2013 at 7:31 PM, Neha nshafi...@wesleyan.edu wrote: Hi, thank you so much!

Re: [gmx-users] How to compile/run Gromacs on native Infiniband?

There's no ibverbs support, s o pick your favorite/best MPI implementation, more than that you can't do. -- Szilárd On Mon, Jun 3, 2013 at 2:54 PM, Bert bert.u...@gmail.com wrote: Dear all, My cluster has a FDR (56 Gb/s) Infiniband network. It is well known that there is a big difference

[gmx-users] Re: Creating a monolayer from Martini bilayer

Hi Tsjerk, Thank you so much for being so patient! I have yet another question. The membrane I got from the Martini website already has water in it. Do I need to add more water and if so why? Also how exactly do I use trjconv to put all molecules in the box? Sorry for being so annoying need a

Re: [gmx-users] CG angle distribution

In my experience parametrizing with the Martini forcefield that works fine. You might have to do it in a iterative manner though, since non-bonded (VDW) iteractions might shift the equilibrium with respect to the value you set (unless you exclude all the problematic non-bonded interactions, of

Re: [gmx-users] Re: Creating a monolayer from Martini bilayer

Hi Neha, You can use trjconv with option -pbc mol to put all molecules in the box. If you want a vacuum, you probably don't want to add more water. But just play with it and see what comes out. CG simulations are fast enough for that kind of trial-and-error. Cheers, Tsjerk On Mon, Jun 3, 2013

[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

Hi guys I am using the set of parameters that I added before and I am getting energy Conservation THANKS John -- View this message in context: http://gromacs.5086.x6.nabble.com/Have-your-ever-got-a-real-NVE-simulation-good-energy-conservation-in-gromacs-tp5008501p5008756.html Sent from the

[gmx-users] Specific question regarding SPC water model

Dear group, I am not sure how SPC energy actually works - is there really just one VdW interaction - just between two oxygen atoms? If so, when I place a hydrogen atom of one water molecule at the location of the oxygen from another water, the two oxygens are separated by the distance of H-O

[gmx-users] eletrical filed issue

Dear Gromacs Developers or Users I am trying to apply a constant electrical field in Gromacs. I have made a charged fullerene in vacuum for testing. A electrical field in x direction is applied as: ; Electric field E-x = 1 2 1 However, the C60 moves only around 0.1 nm in 10 ps and

[gmx-users] About low PH simulation of DPPC liposomes

Hi guys I need to simulate DPPC liposomes in low PH environment I have been looking for literature but I have not found a good option. Any suggestion?? Thanks John Michael -- View this message in context:

[gmx-users] Re: Specific question regarding SPC water model

Thanks for the answer. You're introducing atomic overlap and thus an energetic singularity from the infinite Coulombic attraction. Is there anything I can do with this? I posted this question because I'm trying to run a Monte Carlo simulation of a water box but eventually it finds the global

[gmx-users] assembling trajectory files

Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to continue the first 10 ns simulation. In order to do some analysis , I'm aiming to assemble both trajectory and tpr files. I would be very grateful if someone could help me in this issue. --

Re: [gmx-users] assembling trajectory files

On 6/3/13 8:54 PM, Souilem Safa wrote: Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to continue the first 10 ns simulation. In order to do some analysis , I'm aiming to assemble both trajectory and tpr files. I would be very grateful

Re: [gmx-users] Re: Specific question regarding SPC water model

On 6/3/13 8:12 PM, Someone Else wrote: Thanks for the answer. You're introducing atomic overlap and thus an energetic singularity from the infinite Coulombic attraction. Is there anything I can do with this? I posted this question because I'm trying to run a Monte Carlo simulation of a

Re: [gmx-users] assembling trajectory files

Dear Justin, Thank you very much for your quick reply, that is helpful to me On 4 June 2013 10:05, Justin Lemkul jalem...@vt.edu wrote: On 6/3/13 8:54 PM, Souilem Safa wrote: Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to

[gmx-users] About Concatenation of several trajectory files

Dear Justin, Mark other gromacs users Thank you fro your previuos replies     I need to concatenate several .trr , .xtc and .edr files . Is there is any gromacs tools availble ? or  Is it enough to use cat command  in Linux Thanks In ADVANCE -- gmx-users

Re: [gmx-users] About Concatenation of several trajectory files

On 6/3/13 10:15 PM, vidhya sankar wrote: Dear Justin, Mark other gromacs users Thank you fro your previuos replies I need to concatenate several .trr , .xtc and .edr files . Is there is any gromacs tools availble ? or Is it enough to use cat command

[gmx-users] Re: frame

hi, Wagner It works! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org