Re: [gmx-users] Trying to replicate Aqvist's results (solvation free energy).

first thing that I notice is that you are using PBC whereas Aqvist employed a spherical boundary model. I also think that PME is not applicable for a spherical boundary, so the reciprocal space contributions may be considered as spurious if you want to reproduce the original results. Maybe you shou

Re: [gmx-users] Use pull code to restrain the COM

On 8/8/13 6:43 PM, Bin Liu wrote: Hi All, I would like to restrain the COM of a molecule, say a protein, in my simulation. I found the pull code can do the job. However, I am not sure about several parameters in the .mdp file. For example, if I want to restrain the COM of the protein in only

[gmx-users] Use pull code to restrain the COM

Hi All, I would like to restrain the COM of a molecule, say a protein, in my simulation. I found the pull code can do the job. However, I am not sure about several parameters in the .mdp file. For example, if I want to restrain the COM of the protein in only z direction, but not rigidly, I can sp

Aw: [gmx-users] Umbrella sampling - position restraints

it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart.  A comparison however, would probably

[gmx-users] Trying to replicate Aqvist's results (solvation free energy).

Hello, As we're trying to get familiar with Gromacs, in order to be able to perform solvation free energy calculations of ions, we're trying to replicate the results obtained by Aqvist (the author of the article from which were obtained Lennard-Jones parameters for alkaline and alkaline earth

Re: [gmx-users] Umbrella sampling - position restraints

On 8/8/13 3:57 PM, rookie417 wrote: Dear GROMACS users, I followed the Umbrella Sampling tutorial to run a simple simulation of pulling polymer chain from the surface of micelle. I used position restraints for the initial equilibration, however I realized a typo in the define=-DPOSRES mdp file

[gmx-users] Umbrella sampling - position restraints

Dear GROMACS users, I followed the Umbrella Sampling tutorial to run a simple simulation of pulling polymer chain from the surface of micelle. I used position restraints for the initial equilibration, however I realized a typo in the define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulati

Re: [gmx-users] g_WHAM

On 8/8/13 2:37 PM, Shima Arasteh wrote: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv It's the error what get; File input/output error: tpr-files.dat Then a file named "tpr-files.dat" does not exist in the working directory. Check for typos and the existence of the fil

Re: [gmx-users] g_WHAM

g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv It's the error what get; File input/output error: tpr-files.dat Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Thursday, August 8, 2013 10:

[gmx-users] g_WHAM

Hi, Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM? I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all. I ran such dat file, but doesn't work and gives me an error of n

Re: [gmx-users] g_WHAM

On 8/8/13 2:13 PM, Shima Arasteh wrote: Hi, Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM? I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all. I ran such dat file,

Re: [gmx-users] Re: inconsistent energy drops

On 8/8/13 11:51 AM, Brad Van Oosten wrote: FYI I have done some more experimenting on the problem with different versions and computers running the exact same start .tpr file and this is what ive found: Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops Computer A with 4.6.1 or 4.6.

[gmx-users] Re: Gromacs: GPU detection

I can confirm this, I have noticed this as well. -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-GPU-detection-tp5010308p5010399.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists

[gmx-users] Re: inconsistent energy drops

FYI I have done some more experimenting on the problem with different versions and computers running the exact same start .tpr file and this is what ive found: Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops Computer A with 4.6.1 or 4.6.3 without MPI = no random energy drops Compute

RE: [gmx-users] GPU + surface

Hi, The -testverlet option is only for testing (as the name implies). Please set the mdp option cutoff-scheme = Verlet Also please update to 4.6.3, as this, potential, issue might have already been resolved. With the Verlet scheme the CPU and GPU should give the same, correct or incorrect, resul

[gmx-users] GPU + surface

Dear GMX users. I have done simulation of ions and water near quartz surface (ClayFF) using GPU (GTX580) and Gromacs (4.6.1, single precision, 64 bit, SSE4.1, fftw-3.3.3) and have observed strange behavior of water and ions. Its NVT simulation with freezed surface atoms (see .mdp below) and negat

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

On 2013-08-08 13:17, 朱文鹏 wrote: > Hello David, > > Thank you for your response. > > Do you mean a finite lipid bilayer on a periodic infinite graphene > layer, or a lipid liposome (or a whole spherical cell) on a periodic > infinite graphene layer? A 2D periodic graphene layer - which will be a

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

Hello David, Thank you for your response. Do you mean a finite lipid bilayer on a periodic infinite graphene layer, or a lipid liposome (or a whole spherical cell) on a periodic infinite graphene layer? For the first case, how do you control the surface tension of lipid bilayer? For the second c