Re: [gmx-users] GROMACS 4.6 release is ready!

How nice it is. Cheers. Albert On 01/21/2013 09:09 AM, Mark Abraham wrote: Hi GROMACS users, The day is finally here - GROMACS 4.6 is out! As you've probably heard by now, there are lots of wonderful new performance features, including * a native GPU implementation layer - thanks to some he

[gmx-users] question about fftw3 in gromacs 4.6 installation

Hello: I am compiling the latest gromacs 4.6 with command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC -DCMAKE_C_COMPILER=//soft/openmpi-1.4.3/bin/mpicc -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6 -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=OFF -DFFTW_INCLUDE_DIR=/soft/fftw-3.

[gmx-users] gromacs 4.6 GB/SA problem and poor performance

Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,

[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format

Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box dimensions. It seems that the two tools are quite incompatible, especially when th

Re: [gmx-users] Run long-time MD process

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations On 01/21/2013 11:20 AM, Kieu Thu Nguyen wrote: Dear All, I intend to run a long-time MD process. Can i split it into many smaller processes without losing system properties ? Is that the following process will be followed from t

Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format

probably you can try "catdcd" On 01/21/2013 11:29 AM, Anna Marabotti wrote: Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box di

[gmx-users] Implicit sovent simulation with CHARMM FF

Hi, all I have trouble grompping my systems containing drug-like molecules. I am using Charmm parameter and the addion of atomtypes and pairtypes were all done. Under explicit condition everthing is alright and I also added the missing atomtypes in the gb.itp under the charmm.ff folder like this

[gmx-users] Fw: Implicit sovent simulation with CHARMM FF

Sorry..I'v made a stupid mistake annotating some lines in the .itp file. I'v fixed it. 2013-01-21 supermanczx 发件人： supermanczx 发送时间： 2013-01-21 18:59:20 收件人： gmx-users 抄送： 主题： Implicit sovent simulation with CHARMM FF Hi, all I have trouble grompping my systems containing drug-like

Re: [gmx-users] GROMACS 4.6 release is ready!

That is really great..Thanks for all the work on this! Cheers, Davide On 21/01/13 9:09 AM, "Mark Abraham" wrote: >Hi GROMACS users, > >The day is finally here - GROMACS 4.6 is out! > >As you've probably heard by now, there are lots of wonderful new >performance features, including >* a native G

Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance

On 2013-01-21 09:55, Changwon Yang wrote: Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench

[gmx-users] g_bar Fatal error: There is no proper lambda legend

Dear GROMACS developers, I was using gmx-4.6.b3 to run a simple FEP simulation for calculating the solvation free energy of ions in water. The simulations run ok. However, when I tried to use g_bar with the dhdl.xvg files, I received the following error: "There is no proper lambda legend in file '

Re: [gmx-users] question about fftw3 in gromacs 4.6 installation

On 1/21/13 3:44 AM, Albert wrote: Hello: I am compiling the latest gromacs 4.6 with command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC -DCMAKE_C_COMPILER=//soft/openmpi-1.4.3/bin/mpicc -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6 -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=O

Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote: Dear All, I want to know that my lipid bilayer is equilibrated or not yet. So i want to calculate the change of area per lipid and the bilayer thickness versus time. Which tool or method should i use ? Extract box vectors over time from the .edr f

Re: [gmx-users] g_bar Fatal error: There is no proper lambda legend

On 1/21/13 7:31 AM, Elena Lilkova wrote: Dear GROMACS developers, I was using gmx-4.6.b3 to run a simple FEP simulation for calculating the solvation free energy of ions in water. The simulations run ok. However, when I tried to use g_bar with the dhdl.xvg files, I received the following error

Re: [gmx-users] could not understand force.xvg file

On 1/21/13 8:27 AM, biki wrote: Hi , I am doing a simulation of 32 spce water molecules using Gromacs-4.5.5 version. I need to calculate the force on each hydrogen atom of each water molecule due to all other atoms on rest 31 water molecules. I have generated the force.xvg file and I know t

Re: [gmx-users] question about fftw3 in gromacs 4.6 installation

On 01/21/2013 01:31 PM, Justin Lemkul wrote: Your cmake command needs to use -DFFTWF_INCLUDE_DIR and -DFFTWF_LIBRARY to indicate the single-precision libraries (note that -DFFTW_INCLUDE_DIR and -DFFTWF_INCLUDE_DIR specify different things) or simply use -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3/ for

[gmx-users] Full Hessian matrix in readable format

Hello, fellow Gromacs users! I'm testing a parametrization method that derives the force contsnts for bonds, angles and imporopers from an ab-initio hessian matrix. I would like to print the full hessian matrix (not the diagonalized one) to compare with the ab-initio matrix. Unfortunately, my se

Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance

On Mon, Jan 21, 2013 at 3:55 AM, Changwon Yang wrote: > Im trying to run an md or em using an implicit solvation method using > gromacs 4.6 but I always get the incorrect result. > ICC version : icc 11.0 > fftw version : 3.2.2 > > benchmark system is gromacs-gpubench > gromacs-gpubench-dhfr.tar/C

[gmx-users] how can I make statics for Z-axis?

hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www

Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

Thank Justin ! That is APL. How about bilayer thickness ? I made density.xvg file of headgroup from using g_density. On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul wrote: > > > On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote: > >> Dear All, >> >> I want to know that my lipid bilayer is equilibrated o

Re: [gmx-users] Run long-time MD process

Thank Felipe ! :-) On Mon, Jan 21, 2013 at 5:30 PM, Felipe Pineda, PhD < luis.pinedadecas...@lnu.se> wrote: > http://www.gromacs.org/**Documentation/How-tos/**Extending_Simulations > > > On 01/21/2013 11:20 AM, Kieu Thu Nguyen w

Re: [gmx-users] inquiring for solving trjconv problems

On 1/21/13 11:00 AM, Mehdi Bagherpour wrote: hello justin I used *make_ndx -f md.tpr: 0 System : 35194 atoms 1 DNA : 1012 atoms 2 MG : 4 atoms 3 CL :29 atoms 4 K :51 atoms 5 Water

Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote: Thank Justin ! That is APL. How about bilayer thickness ? I made density.xvg file of headgroup from using g_density. g_dist with index groups specifying however you want to define the boundaries for the membrane, or (shameless plug) a lateral proj

Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

Hi, Not sure why, but it looks like libcudart.so is linked against a glibc that not compatible with what you have (perhaps much newer)? Alternatively you could try adding "--add-needed" to the linker flags, but I doubt it will help. Cheers, -- Szilárd On Mon, Jan 21, 2013 at 5:09 PM, James St

[gmx-users] Getting the virial for each individual atom.

Hello, For the research I'm working with, I need to get the virial for each individual atom in the system. I've been tracing all of the calls made in the methods related to virials(Version 4.5.5) and this is the call stack that I think has what I need. mdrun.c -> do_md in md.c -> do_force in sim_u

RE: [gmx-users] Getting the virial for each individual atom.

Hi, The virial has no meaning per atom. And you can't get the virial per atom out of Gromacs, it is never calculated in that way (see the manual for details). A special local pressure version of Gromacs exists, but even there you won't get a virial per atom. Cheers, Berk

Re: [gmx-users] Getting the virial for each individual atom.

Berk, Here is where I think I might be able to: In calcvir.c there is a method called calc_vir which takes, among other things, int nxf(no idea what this does), rvec x[], and revec f[]. It then does dvxx+= x[i][xx] *f[i][XX];. This is the same as the formula that I am trying to solve for (Vi*Pi +

[gmx-users] Digedral Angle for aa?

How can we Plot the X1,X2 angle (degree) wise time point for single amino acids? Can g_angle or g_chi can do ?-- 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

Re: [gmx-users] Digedral Angle for aa?

On 1/21/13 1:08 PM, 라지브간디 wrote: How can we Plot the X1,X2 angle (degree) wise time point for single amino acids? Can g_angle or g_chi can do ? g_angle seems to be the most straightforward way. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist

Re: [gmx-users] Getting the virial for each individual atom.

On Mon, Jan 21, 2013 at 7:06 PM, Marcin, Zachary wrote > dvxx+= x[i][xx] *f[i][XX]; > Compare the indexing above with: > This is the same as the formula that I am trying to solve for (Vi*Pi + > .5*SUM(Rij * Fij)). > ... the ones you want to have. See the difference ? The existing code takes on

Re: [gmx-users] clusterization in dihedral space

On 1/21/13 1:54 PM, francesco oteri wrote: Dear gromacs users, I am trying to run dihedral space clustering with g_dih, but I found that it gives me a lot of error like: Dihedral around 24,26 not found in topology. Using mult=3 Looking on the net, I found something alarming: g_dih is gromos sp

Re: [gmx-users] clusterization in dihedral space

Thank you, but I don't see how performing cluster analysis with g_angle Francesco 2013/1/21 Justin Lemkul > > > On 1/21/13 1:54 PM, francesco oteri wrote: > >> Dear gromacs users, >> I am trying to run dihedral space clustering with g_dih, >> but I found that it gives me a lot of error like: >

Re: [gmx-users] clusterization in dihedral space

On 1/21/13 2:06 PM, francesco oteri wrote: Thank you, but I don't see how performing cluster analysis with g_angle You may have to do some post-processing yourself, but g_angle can certainly measure dihedrals and produce distributions. -Justin --

Re: [gmx-users] Getting the virial for each individual atom.

Zach, Do you have periodic system with charges? For PBC, you might try one of the forms in J. Chem. Phys. 131 154107 (2009). Electrostatics are more work... For Ewald sum and PPPM contribution, you could check refs in lammps.sandia.gov/doc/PDF/kspace.pdf We have an upcoming paper that explains in

[gmx-users] Parallelization scheme and terminology help

I have been lost in the sea of terminology for installing gromacs with multi-processors. The plan is to upgrade from 4.5.5 to the 4.6 and i want the optimal install for my system. There is a a nice explanaion at http://www.gromacs.org/Documentation/Acceleration_and_parallelization but the nu

Re: [gmx-users] Parallelization scheme and terminology help

On Mon, Jan 21, 2013 at 11:50 PM, Brad Van Oosten wrote: > I have been lost in the sea of terminology for installing gromacs with > multi-processors. The plan is to upgrade from 4.5.5 to the 4.6 and i want > the optimal install for my system. There is a a nice explanaion at > http://www.gromac

Re: [gmx-users] inquiring for solving trjconv problems

Hello Justin My problem is fixed I am very grateful for your help. I used from bellow commands: * * *1- make_ndx -f md.tpr * *>r 1-16 ->DNA have 32 residue 2- trjconv -s md.tpr -f wi_md.xtc -n index.ndx -o md.pdb -center -pbc mol * *2-1- for centering ---> residue 1-16 ---> new group

[gmx-users] Re: gromacs 4.6 GB/SA problem and poor performance

Input files: conf.gro and mdp files http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM cpu-imp-RF-inf.mdp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 0 nstlist = 0 ns_type

Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

Thank Justin ! And i used GridMAT-MD as you advised. I got result "The average bilayer "thickness" will be printed to 50x50_average_pbc.dat". But that result is only equal to a half of experiment result. I think "bilayer thickness" is equal to the sum of "top leaflet thickness" and "bottom leaflet