Re: [gmx-users] Amber to Gromacs conversion

2013-12-10 Thread Chetan Mahajan
This tool seems to be working. No errors so far. Thanks Chetan On Tue, Dec 3, 2013 at 9:32 PM, Barnett, James W. jbarn...@tulane.eduwrote: Right, but according to the error message you need at least Python 2.6. jbarn...@tulane.edu | from mobile Chetan Mahajan chetanv...@gmail.com wrote:

Re: [gmx-users] redmine account

2013-12-10 Thread Patrick Fuchs
Thanks Roland, it works now. Patrick Le 09/12/2013 23:26, Roland Schulz a écrit : Hi, sorry we had a mixup with the account activation. Your account should be activated now. Roland On Mon, Dec 9, 2013 at 3:35 AM, Patrick Fuchs patrick.fu...@univ-paris-diderot.fr wrote: Hi all, I tried

[gmx-users] deformation in cnt

2013-12-10 Thread Atila Petrosian
Dear Justin Based on your suggestion, I added C-C bond length to z dimension of box (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). Then I used genion to neutralize system using replacing 2 water molecules by 2 Na ions, gro file obtained from genion is strange. When I see this gro file by vmd,

Re: [gmx-users] pressure based replica exchange

2013-12-10 Thread João Henriques
Hi there, In theory you may use any parameter in the Hamiltonian, but I'm pretty sure Gromacs' REMD applies parallel tempering for temperature only. I never looked at the actual code, but I wouldn't be surprised if it didn't even check for differences in pressure between replicas and that's why

[gmx-users] Trouble running 4.6.4. on cpu+gpu but not on gpu alone

2013-12-10 Thread rajat desikan
Dear all, I recently installed gromacs 4.6.4 on our cluster. The configuration is 12 cpus and 2 gpus per node. The build details are given below. I am able to run gromacs on the 2 gpus alone. However, running a job with cpu+gpu fails with a fatal error (given below). Gromacs build: cmake ..

Re: [gmx-users] pressure based replica exchange

2013-12-10 Thread Mark Abraham
On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Dear All, Is it possible to do pressure based replica exchange simulations in gromacs? Basically I want to do replica exchange simulations for my membrane system at different surface tensions. If I just set different

Re: [gmx-users] Trouble running 4.6.4. on cpu+gpu but not on gpu alone

2013-12-10 Thread Carsten Kutzner
Hi, start with using as many MPI processes as you have GPUs. GROMACS will use several OpenMP threads per MPI process to use all your CPU cores. You can also do that manually with mpirun -np 2 mdrun-mpi -ntomp 6 Carsten On 12/10/2013 10:30 AM, rajat desikan wrote: Dear all, I recently

Re: [gmx-users] deformation in cnt

2013-12-10 Thread Dr. Vitaly Chaban
If the system does not explode, everything is correct. Though your solution is perhaps in the wrong place in relation to the tube. Dr. Vitaly V. Chaban On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Justin Based on your suggestion, I added C-C bond

[gmx-users] Normal Mode Analysis with Gromacs 4.6

2013-12-10 Thread mcfc1301
Hello Everyone, I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but find little useful. My Gromacs was installed in a Linux cluster. Follows is my steps to do normal mode analysis: • pdb2gmx -ignh -ff forcefield -f 1SHS mutated.pdb -o mut.gro -p topol.top • editconf

Re: [gmx-users] Fwd: Normal Mode Analysis

2013-12-10 Thread Joaquim Rui de Castro Rodrigues
Dear Sathish, You are writing vectors 7-100 to eigenvec.trr using g_nmeig, and then ask g_anaeig_d to analyze the 7th vector of eigenvec.trr. Try running g_nmeig_d with default parameters: g_nmeig_d -f hessian.mtx -s nm.tpr and then generate an oscillating trajectory with g_nmtraj_d -s nm.tpr

[gmx-users] what is the mean sar, st, pi, gar and hct of gbsa.itp?

2013-12-10 Thread C.H. Kim
Dear All. Hi. I'm want calculation of dimer protein. My proteins have manganese. But don't have gbsa.itp of manganese. I'm insert Mn data, but I don't know 'sar, st, pi ...' What is the values mean? Thank you. -- View this message in context:

[gmx-users] ligand covalently bond with the protein

2013-12-10 Thread aixintiankong
Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] what is the mean sar, st, pi, gar and hct of gbsa.itp?

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 8:11 AM, C.H. Kim poc...@icloud.com wrote: Dear All. Hi. I'm want calculation of dimer protein. My proteins have manganese. But don't have gbsa.itp of manganese. I'm insert Mn data, but I don't know 'sar, st, pi ...' What is the values mean? Please read manual

Re: [gmx-users] ligand covalently bond with the protein

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 7:54 AM, aixintiankong aixintiank...@126.comwrote: Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much !

Re: [gmx-users] why it is symmetric

2013-12-10 Thread Justin Lemkul
On Mon, Dec 9, 2013 at 12:58 PM, Albert mailmd2...@gmail.com wrote: Hello: I am calculating the water density inside my membrane protein along Z directions. I used the a_ri3DC tool in Gridcount which is a patch in Gromacs for calculation: a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp

Re: [gmx-users] OPLS force field issue

2013-12-10 Thread Justin Lemkul
On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi es...@sfu.ca wrote: Thanks Justin. I added the bond description in the ffbonded.itp but it does not show in the topol.top file. In ffbonded.itp we have: [ bondtypes ] ; ij func b0 kb OWHW 10.09572

Re: [gmx-users] deformation in cnt

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Justin Based on your suggestion, I added C-C bond length to z dimension of box (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). Then I used genion to neutralize system using replacing 2 water molecules by 2

[gmx-users] Strange trjconv error

2013-12-10 Thread rajat desikan
Hi All, I have a NPT NAMD trajectory of a membrane-protein that I want to analyze in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb and generated a .top from the .psf using topotools in vmd. I then generated a .tpr using grompp When I do any simple gromacs command like:

Re: [gmx-users] Strange trjconv error

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I have a NPT NAMD trajectory of a membrane-protein that I want to analyze in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb and generated a .top from the .psf using topotools in vmd. I

[gmx-users] Computing the energy of interaction

2013-12-10 Thread Golshan Hejazi
I have a paracetamol crystal and I would like to estimate the paracetamol/paracetamol energy of interaction per unitcell.  To do this I am doing the following: Energy of interaction of paracetamols per unitcell=  Total energy of a unitcell - (Energy of a molecule in the unitcell* number of the

Re: [gmx-users] constraining protein in the box

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 12:31 PM, Shine A shin...@iisertvm.ac.in wrote: Sir, I completed a 400 ns MD simulation. But in some part of the trajectory my protein is just out side the box I selected (triclinic). Is there any option in gromacs to constrain my protein in box during simulation.

Re: [gmx-users] constraining protein in the box

2013-12-10 Thread jkrieger
This is probably a visualisation problem not a simulation problem. You may just need to process the simulation with trjconv using -pbc nojump. Sir, I completed a 400 ns MD simulation. But in some part of the trajectory my protein is just out side the box I selected (triclinic). Is there

[gmx-users] ligand covalently bond with the protein

2013-12-10 Thread aixintiankong
Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] ligand covalently bond with the protein

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 7:28 PM, aixintiankong aixintiank...@126.comwrote: Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! Please refer to the link

Re: [gmx-users] Strange trjconv error

2013-12-10 Thread rajat desikan
Dear Justin, Thanks for the suggestion. Producing a .trr in catdcd still failed because it apparently produces a trajectory without a timestamp. So, I loaded the .dcd into vmd and saved the coordinates in a .trr file. This worked like a charm :) Note to self: Install gromacs with the vmd plugin