Re: [gmx-users] can we differentiate it?

Hi Tsjerk: many thanks for your such helpful advices. If I Turn off PBC in Z-direction, I am just wondering, is it possible to add different salt in each leaflet? For instance: 0.15M NaCl in the up leaflet and 0.15M KCl in the low leaflet? When I use genion command in Gromacs, I don't find an

[gmx-users] Aquaporin in DOPC

I was able to do the KALP-15 in DPPC. Thanks to the tutorial by Justin Lemkul. Now, I tried to do it with a different protein and lipid. I used aquaporin (protein) and DOPC (lipid) I now have the solvated Aquaporin in DOPC. Now, I'm wondering, should I put ions too? to neutralize the system? If yes

[gmx-users] Problems with mdrun (version 4.6.5) and CPU-type: Xeon E5472

Thank you for the suggestion. That solved the problem. If I understand it correctly GMX_DISTRIBUTABLE_BUILD=ON only disables the support for 'rdtscp', which is used for determining the wall-time. Does this effect the determination of the wall-time? Meaning when one uses GMX_DISTRIBUTABLE_BUILD

[gmx-users] g_helixorient help

Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace

[gmx-users] graphics card fail during mdrun

Hello! I was running a simulation using both of the graphics cards on my desktop (I have one Tesla C2075 and one Quadro 2000, which also handles monitor output). I am pretty sure the Quadro 2000 has failed this morning, and I was wondering, what happens to an mdrun in progress when one of the grap

Re: [gmx-users] can we differentiate it?

No, but genion asks you for a group of solvent molecules to use as the candidates for replacement. You wish to differentiate two different sub-groups, which you can do in advance in your genion -n file, e.g. generated using a geometric criterion in g_select. This kind of Unix-style re-use is why we

Re: [gmx-users] graphics card fail during mdrun

The behavior of most programs in case of a hardware failure is undefined. However, as an MD simulation is quite sensitive to data corruption, the simulation will most often crash immediately after such an event. However, I can also imagine that mdrun ends up hanging, e.g. waiting for data from the

Re: [gmx-users] Aquaporin in DOPC

On 1/27/14, 4:02 AM, jhosamelly wrote: I was able to do the KALP-15 in DPPC. Thanks to the tutorial by Justin Lemkul. Now, I tried to do it with a different protein and lipid. I used aquaporin (protein) and DOPC (lipid) I now have the solvated Aquaporin in DOPC. Now, I'm wondering, should I put

Re: [gmx-users] Rerun error

Does it mean that doing rerun on current md_0_1.trr file is impossible, unless it is transfered to a cluster or a more powerful system? Sincerely, Shima On Sunday, January 26, 2014 11:50 AM, Mark Abraham wrote: Hi, Thanks for the full description. It seems like your file system cannot hand

Re: [gmx-users] Rerun error

Yes. You need to read the positions to do a rerun. To do that, you need to be able to read the file. Mark On Mon, Jan 27, 2014 at 7:25 PM, Shima Arasteh wrote: > Does it mean that doing rerun on current md_0_1.trr file is impossible, > unless it is transfered to a cluster or a more powerful sys

Re: [gmx-users] Pull code vs. manual pull for umbrella sampling

Hello, As I had explained earlier, I have done MD at varied protein bi-layer distances. I now want to create a probability distribution histogram along the reaction coordinate I generated by varying the distances. I know I can concatenate various .trr files I have from various MD runs with diffe

Re: [gmx-users] Pull code vs. manual pull for umbrella sampling

On 1/27/14, 3:49 PM, shivangi nangia wrote: Hello, As I had explained earlier, I have done MD at varied protein bi-layer distances. I now want to create a probability distribution histogram along the reaction coordinate I generated by varying the distances. I know I can concatenate various .

[gmx-users] free energy calculations for reference state for constant pH MD simulations...

Hello, I am trying to run constant pH MD with GROMACS, and started with the TI free energy calculations. I am following Justin Lemkul`s free energy calculation tutorial, and assuming that the free energy calculations will be similar to calculate the protonation energy of titratable amino acids

[gmx-users] multiple GPU on multiple nodes

Hi guys I am using a CrayXK7 machine with one GPU (Tesla K20) per node (one AMD Opteron 16-core Interlagos x86_64). Currently I am trying to run the gromacs gpu version using only two nodesbut it is not working. When I tried using one node and one gpu it works aprun -n 1 mdrun_mpi -deffnm filenam

Re: [gmx-users] multiple GPU on multiple nodes

You need to export the CRAY_CUDA_PROXY or CRAY_CUDA_MPS (e.g. on Blue Waters) environment variable which enables multiple ranks to use the same GPU. You are running a binary compiled without CPU SIMD support (i.e. GMX_CPU_ACCELERATION=None instead of AVX_128_FMA) as the console output notes. This

[gmx-users] Error in grompp for protein-ligand tutorial

I am new to Gromacs, then follow the tutorial protein-ligand, decided to adapt the procedure for my protein (acetylcholinesterase) and my binder. The procedure is this (protein-ligand complex): http

Re: [gmx-users] Pull code vs. manual pull for umbrella sampling

Dear Justin, Thanks for the reply. I have a follow up question. I used g_dist to obtain the COM distance between the protein and bi-layer at one particular starting configuration. As you suggested, I fed the dist.xvg file into g_analyze. However, the output from g_analyze i.e. distr.xvg file c

Re: [gmx-users] Pull code vs. manual pull for umbrella sampling

I see this when I run g_analyze command: SS1 6.104595e+00 5.846878e-01 2.386978e-02 -0.151 -0.227 SS2 8.228340e-01 3.035145e+00 1.239093e-01 -0.283 -0.417 SS3 6.970040e-01 3.047464e+00 1.244122e-01 -0.347 -0.411 SS4 -4.231055e+00 2.099952e-01 8.573016e-0

[gmx-users] At what point is the random seed generated?

Hi, When using 'gen-seed = -1' at what point is the random seed assigned? e.g. Does it use the process ID of grompp and embed the seed number in the tpr file, or does it use the process ID of mdrun? I ask because I have 50 identical simulations started from the same tpr file :( Thanks, -Trayder

Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...

See the section "5.7.4 Topologies for free energy calculations" in Gromacs 4.6.5 manual. On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet wrote: > Hello, > > I am trying to run constant pH MD with GROMACS, and started with the TI > free energy calculations. I am following Justin Lemkul`s free e

Re: [gmx-users] At what point is the random seed generated?

On 2014-01-28 08:37, Trayder Thomas wrote: Hi, When using 'gen-seed = -1' at what point is the random seed assigned? e.g. Does it use the process ID of grompp and embed the seed number in the tpr file, or does it use the process ID of mdrun? I ask because I have 50 identical simulations started