[gmx-users] Illegal instruction flag raised in GMX 5.0.4

Hi! In the process of trying to simulate phosphorylated serines I installed gromacs 5.0.4 because I was running into problems with pdb2gmx command not able to merge files. After installation I ran a test command and got the error below. I am kinda lost as to what could be happening!! I would appre

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 97

Hi Tsjerkthank you very much ! as you said, the protein get splite and i can't get it back wiht command 'trjconv -pbc nojump -center'. however, i can use the command 'trjconv -fit rot+trans' to get the protein back. i don't know what the reason is. is my system broken?thank you very much! >

Re: [gmx-users] Installing GTX 980 on linux - which distro should i use?

Le 22/12/2014 17:47, Carlos Navarro Retamal a écrit : I just bought a workstation with 2 GTX 980 (in order to improve my simulations on gromacs), but i’m not able to install it properly. I first start with Centos 7, but my motherboard has an issue with this version, so i couldn’t pass the boot

Re: [gmx-users] Installing GTX 980 on linux - which distro should i se?

Dear everyone, Thanks a lot for all your help. I tried Mr. Mohammad said without luck (maybe the problem is due i have 2 graphic cards? ), In any case, i’ll try with Scientific linux now.. Best regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Unive

Re: [gmx-users] Installing GTX 980 on linux - which distro should i use?

Hi, We use Ubuntu, but recommend against using any of the apt or deb based cuda support, and prefer the bundle of SDK stuff you get from the Nvidia website that you run, shell-script style. In any case, get the latest distro flavour, the latest supported CUDA on it, and the latest gcc compiler CUD

Re: [gmx-users] Installing GTX 980 on linux - which distro should i use?

I personally tried this one: http://www.quantstart.com/articles/Installing-Nvidia-CUDA-on-Ubuntu-14-04-for-Linux-GPU-Computing Please notice that GTX 980/970 has specific CUDA release. Sent with MailTrack

Re: [gmx-users] Installing GTX 980 on linux - which distro should i use?

Hi Carlos, we are mostly using Scientific Linux (v. 6.4) . Carsten On 22 Dec 2014, at 17:47, Carlos Navarro Retamal wrote: > Dear gromacs users, > First of all, if this question doesn’t belong here please feel free to erase > it from the mailist. > I just bought a workstation with 2 GTX 98

[gmx-users] Installing GTX 980 on linux - which distro should i use?

Dear gromacs users, First of all, if this question doesn’t belong here please feel free to erase it from the mailist. I just bought a workstation with 2 GTX 980 (in order to improve my simulations on gromacs), but i’m not able to install it properly. I first start with Centos 7, but my motherbo

[gmx-users] qm-mm calculation : Gromacs + cpmd

Hello, I am planning to qm mm simulation with Gromacs + cpmd. Can I interface recent gromacs version (4.5.5) with cpmd (3.17.1)? Where can I find the information about interface? Thanks, Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mail

[gmx-users] Regarding Null free energy values in Free energy perturbation (bond force constant perturbation)

Hi all, I am trying to perform a free energy perturbation calculation (using Gromacs 4.6.3) to perturb the force constant of a bond (in vaccum), using the B-state parameters in the topology as follows: [ bonds ] ; ai aj funct c0 c1c0B c1B 342

Re: [gmx-users] minimal distance between periodic images

Hi Jinxin, The distance should be at least half of the cut-off distance, such that the total distance (twice the distance between protein and 'box edge') will be larger than the cut-off distance. So you should be fine. Now, if the system undergoes large conformational changes, that may still cause

[gmx-users] minimal distance between periodic images

Dear everyone, During my simulation, i set the option '-d 1.2' creates a buffer of 1.2 nm between the outside of the protein and the edge of the box. In the mdp file, i set the rcoulomb=rvdw=1.4, cutoff-scheme = Verlet. After the simulation, i use g_mindist -pi to analyzed the minimal d

[gmx-users] fluid flow

Hi all - I'm simulating a layer of water above a layer of polymer melt. I want to impose a shear flow on the water to see what happens to the water mixed in with the polymer. What is the best way to do this? Deform, accelerate, or some other option? Thanks Katie -- Gromacs Users mailing li

Re: [gmx-users] PCA of crystal structures

Hi, you can directly project the crystal structures onto the eigenvectors from the PCA with gmx anaeig. It may be necessary to create an index file for each PDB file with an index group that identifies the atoms that correspond to the vector components. Make sure that the order of atoms is the