[gmx-users] Error in pdb2gmx

Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro) I used 13. GROMOS 53a6 force field "Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it mi

[gmx-users] Re: how is the pulling force measured

Hi Alex, I read the manual but I got confused with the details. My pull_geometry = position with pulling direction along y. I am trying to dissociate two interacting proteins. So I set the last amino acid of one protein as my reference group and the last amino acid of the other protein as the pul

[gmx-users] Fatal error: Failed to lock: md.log. Function not implemented.

Hi, when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not equilibration, so I extend NVT simulation as follows: tpbconv -s nvt.tpr -extend 2000 -o next1.tpr mpirun -np 4 mdrun_mpi -reprod -s next1.tpr -cpi nvt.cpt after finish this extending, I got files: traj.trr stat

Re: Aw: [gmx-users] Order of atoms in topology

On 4/29/13 8:34 PM, Mark Abraham wrote: I do not see that the caption to figure 4.8 implies a "reference" atom. It Sorry, loose terminology after a long day. "Reference atom" is a poor choice. What I meant was with respect to the way pdb2gmx constructs impropers - the central atom (i.e. th

Re: Aw: [gmx-users] Order of atoms in topology

I do not see that the caption to figure 4.8 implies a "reference" atom. It talks merely about the angle between planes i-j-k and j-k-l. That angle is signed and the sign is significant for equation 4.60. Does the sign of the angle differ from that between l-k-j and k-j-i? I think not, but it's way

Re: Aw: [gmx-users] Order of atoms in topology

On 4/29/13 8:00 PM, Mark Abraham wrote: On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul wrote: Please start a new thread if you're going to introduce a new topic. I have changed the subject to something more relevant. On 4/29/13 4:23 PM, lloyd riggs wrote: *Dear All,* *Doing a water/tem

Re: Aw: [gmx-users] Order of atoms in topology

On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul wrote: > > Please start a new thread if you're going to introduce a new topic. I > have changed the subject to something more relevant. > > On 4/29/13 4:23 PM, lloyd riggs wrote: > >> *Dear All,* >> *Doing a water/temp energy minimization just for

Re: Aw: [gmx-users] Order of atoms in topology

Please start a new thread if you're going to introduce a new topic. I have changed the subject to something more relevant. On 4/29/13 4:23 PM, lloyd riggs wrote: *Dear All,* *Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ra

Aw: [gmx-users] Re: how is the pulling force measured

    Dear All, Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ran into a bizzar question. So I found its possible by accident to define improper dihedrails forwards and backwards without gromacs complaining, such as atom 1 2 3 4 a

[gmx-users] dummy atom fep topology

Dear All, I wanna perform TI and use dummy atoms. I have seen that a lot of people use in the dummy topology bonded parameters like in the original system. Lets say we have a c3-hc that goes to c3-du then in dummy topology the c3-du bond will be the same as in c3-hc. But in this way my question

[gmx-users] Re: how is the pulling force measured

kim2811 wrote > Hi, > > I am not sure if I quite understand what reference group and pulling group > mean in COM pulling. For the version GROMACS 4.X, I specified in my .mdp > file the pull_ngroup = 1, and then I have my pull_group0 and pull_group1. > Am I right in saying that the pull_group0 is f

[gmx-users] how is the pulling force measured

Hi, I am not sure if I quite understand what reference group and pulling group mean in COM pulling. For the version GROMACS 4.X, I specified in my .mdp file the pull_ngroup = 1, and then I have my pull_group0 and pull_group1. Am I right in saying that the pull_group0 is fixed and only the pull_gro

[gmx-users] Re: genbox box size problem

Justin Lemkul wrote > I have seen this exact problem posted before. The coordinates of the > water box > provided by MARTINI have some coordinate values that basically coincide > across > the periodic box. With genconf, you can apply the -dist option to space > them > out slightly, then re-equ

Re: [gmx-users] ATP/Mg+2 parameters

HI George, For AMBER you can use the parameters by Meagher, Redman, and Carlson they were developed with this force field in mind. They are available on the Bryce group amber parameter database below, although you will have to port them to Gromacs format yourself. http://www.pharmacy.manchester

Re: [gmx-users] GPU job often stopped

On Mon, Apr 29, 2013 at 3:51 PM, Albert wrote: > On 04/29/2013 03:47 PM, Szilárd Páll wrote: >> >> In that case, while it isn't very likely, the issue could be caused by >> some implementation detail which aims to avoid performance loss caused >> by an issue in the NVIDIA drivers. >> >> Try runnin

[gmx-users] Re: GROMACS 4.5.7 released

Hi GROMACS users, The 4.5.7 tarball at the link below has been updated to include the files necessary to build with "configure" in the usual 4.5.x way. (Thanks, Rossen!) The code itself is unchanged - you do not need to rebuild GROMACS 4.5.7 if you have already built using CMake. So that you can v

Re: [gmx-users] GPU job often stopped

On 04/29/2013 03:47 PM, Szilárd Páll wrote: In that case, while it isn't very likely, the issue could be caused by some implementation detail which aims to avoid performance loss caused by an issue in the NVIDIA drivers. Try running with the GMX_CUDA_STREAMSYNC environment variable set. Btw, we

Re: [gmx-users] GPU job often stopped

In that case, while it isn't very likely, the issue could be caused by some implementation detail which aims to avoid performance loss caused by an issue in the NVIDIA drivers. Try running with the GMX_CUDA_STREAMSYNC environment variable set. Btw, were there any other processes using the GPU whi

Re: [gmx-users] GPU job often stopped

On 04/29/2013 03:31 PM, Szilárd Páll wrote: The segv indicates that mdrun crashed and not that the machine was restarted. The GPU detection output (both on stderr and log) should show whether ECC is "on" (and so does the nvidia-smi tool). Cheers, -- Szilárd yes it was on: Reading file heavy.

Re: [gmx-users] GPU job often stopped

On Mon, Apr 29, 2013 at 2:41 PM, Albert wrote: > On 04/28/2013 05:45 PM, Justin Lemkul wrote: >> >> >> Frequent failures suggest instability in the simulated system. Check your >> .log file or stderr for informative Gromacs diagnostic information. >> >> -Justin > > > > my log file didn't have any

Re: [gmx-users] GPU job often stopped

On 04/28/2013 05:45 PM, Justin Lemkul wrote: Frequent failures suggest instability in the simulated system. Check your .log file or stderr for informative Gromacs diagnostic information. -Justin my log file didn't have any errors, the end of topped log file something like: DD step 225

Re: [gmx-users] GPU job often stopped

Hello: yes, I tried the CPU only version, it goes well and didn't stop. I am not sure whether I have ECC on or not. There are 4 Tesla K20 and one GTX650 in the workstation, after compilation, I simple submit the jobs with command: mdrun -s md.tpr -gpu_id 0234 I submit the same system in a

Re: [gmx-users] GPU job often stopped

Have you tried running on CPUs only just to see if the issue persists? Unless the issue does not occur with the same binary on the same hardware running on CPUs only, I doubt it's a problem in the code. Do you have ECC on? -- Szilárd On Sun, Apr 28, 2013 at 5:27 PM, Albert wrote: > Dear: > >

Re: [gmx-users] Re: Illegal instruction (core dumped) - trjconv

This error means that your binaries contain machine instructions that the processor you run them on does not support. The most probable cause is that you compiled the binaries on a machine with different architecture than the one you are running on. Cheers, -- Szilárd On Mon, Apr 29, 2013 at 11

Re: [gmx-users] umbrella sampling tutorial

On 4/29/13 6:42 AM, Shima Arasteh wrote: Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this.

Re: [gmx-users] genbox box size problem

On 4/29/13 5:30 AM, Alexander Björling wrote: Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased

[gmx-users] umbrella sampling tutorial

Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this. Thanks in advance. Sincerely, Shima  --

Re: [gmx-users] genbox box size problem

genbox works best when the box size of the solute is defined as the same as of the water one used to solvate it. So you can build a water box with the dimensions you want and them use it. You can build a water box by using genconf -nbox and use a script to cut to the dimensions you need, mini

[gmx-users] genbox box size problem

Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased the box size things started going wrong. As the s

[gmx-users] Re: Illegal instruction (core dumped) - trjconv

On Mon, Apr 29, 2013 at 10:11 AM, Steven Neumann wrote: > Dear Gmx Users, > > I produced my trajectory using Gromacs 4.6 on GPUs. > When I try: > > trjconv -s md298_gpu.tpr -f md298_gpu.xtc -pbc mol -ur compact -o > md298_gpuURcomp.xtc > > Select a group: 0 > Selected 0: 'System' > Reading frame

[gmx-users] Illegal instruction (core dumped) - trjconv

Dear Gmx Users, I produced my trajectory using Gromacs 4.6 on GPUs. When I try: trjconv -s md298_gpu.tpr -f md298_gpu.xtc -pbc mol -ur compact -o md298_gpuURcomp.xtc Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of md298_gpu.xtc is 0.001 (nm) Using output p

Re: [gmx-users] ATP/Mg+2 parameters

Hello George, You need to use Antechamber, a software provided by the amber developers in a free Amber Tools package. That will produce the right parameters for the Amber force feild. Cheers Abhishek Hello Joao > > Thanks for the reply; I am planning to use Amber 99SB-ILDN force field. > > I jus