Re: [gmx-users] mdrun GPU

Hi, For NVIDIA GPUs you should use their drivers and a CUDA build. It looks like you are using other drivers and an OpenCL build, which is completely untested. Mark On Mon, 20 Nov 2017 06:51 Ragothaman Yennamalli wrote: > Hi, > I have been reading this ( > >

Re: [gmx-users] Energy analysis

Yes Dr. Dallas, I have gone through free energy analysis tutorial, But I'm wondering that whether this tutorial is working for large molecule like protein or not? Because the tutorial has explained methane only. Your feedback will highly be appreciated. Thanks! Amir On Sun, Nov 19, 2017 at

[gmx-users] mdrun GPU

Hi, I have been reading this ( http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html) and trying to run mdrun in a GPU based system. Unfortunately, I don't understand what the error is and how to troubleshoot it. Copy pasted below is the output I got for gmx mdrun. I tried

Re: [gmx-users] Energy analysis

Always a good starting point http://www.gromacs.org/Documentation/Tutorials Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

Re: [gmx-users] Energy analysis

Thanks Mark, Depends what you mean by "stability." Actually, I don't know the role of metal ion if it is used as co-factor by a particular protein. I thought to do comparative analysis by MD simulation which might predict the possible role of metal (in this case Zn^2+). Other analysis like RMSD,

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, You can't decompose the "turning off" in the FE code by groups. You can turn off the coulomb in the protein, but that turns off its interactions with itself, solvent, and anything else Mark On Sun, Nov 19, 2017 at 9:27 PM Justin Lemkul wrote: > > > On 11/19/17 3:42 PM,

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

On 11/19/17 3:42 PM, Mark Abraham wrote: Hi, Oh, I see. Yes that feature turns off both kinds of non-bonded interactions. Then there is nothing useful for what you want. Couldn't this be done with the free energy code? Turn off protein-water electrostatics by running in the lambda=1 state

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, Oh, I see. Yes that feature turns off both kinds of non-bonded interactions. Then there is nothing useful for what you want. Mark On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan wrote: > Hi Mark, > > I apologize if I did not describe my problem correctly the first

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi Mark, I apologize if I did not describe my problem correctly the first time, but I need the VdW interactions to stay on between all atoms at all times. I only need to turn off the electrostatic interactions between water and proteins. Thanks, Aram Hi, > > You've described the feature

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, You've described the feature correctly. Whether it is useful in a study design is another matter :-) Mark On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan wrote: > Hi Mark, > > I am not sure I understood. If I for example say "energygrp-excl = Protein > Water" would

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi Mark, I am not sure I understood. If I for example say "energygrp-excl = Protein Water" would not I turn off all the non-bonded interactions between water and protein? Or did you mean something else? Thanks, Aram > Hi, > > In the group scheme you can turn on energy-group exclusions to get

Re: [gmx-users] Energy analysis

Hi, Depends what you mean by "stability." A well designed study could seek to measure or estimate the difference in the free-energy of folding, but that would probably require an infeasibly large amount of sampling, and be highly dependent on the quality of the parameterization of the

Re: [gmx-users] CgenFF conversion failed

For those interested, the issue is in the NetworkX 2.0 package for Python. Version 1.11 produces correct output, but 2.0 fails. I suspect this is the root issue of all the recent complaints about the conversion script failing. Thanks to Albert for helping debug this finally. -Justin On

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hi, In the group scheme you can turn on energy-group exclusions to get this working, but of course all of those states are sampling unphysical things from a broken forcefield. That can be OK, but you will have to be able to defend that claim. Mark On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan

Re: [gmx-users] CgenFF conversion failed

file sent to you private email address. thx a lot On 11/19/2017 06:06 PM, Justin Lemkul wrote: On 11/19/17 11:34 AM, Albert wrote: Hello, I generated a ligand.str file from Parachem website. Then, I try to convert it to Gromacs format with command line: >cgenff_charmm2gmx.py UNK

Re: [gmx-users] CgenFF conversion failed

On 11/19/17 11:34 AM, Albert wrote: Hello, I generated a ligand.str file from Parachem website. Then, I try to convert it to Gromacs format with command line: >cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff However, the job always failed with the following messages:

Re: [gmx-users] Determining the cut offs more than half of the box

On 11/19/17 3:17 AM, Iman Ahmadabadi wrote: Dear Mr.Mark Abraham, Thank you for your help. Because of the accuracy of the results, I should use a reasonable cut offs for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too small for my project because of the importance of

[gmx-users] CgenFF conversion failed

Hello, I generated a ligand.str file from Parachem website. Then, I try to convert it to Gromacs format with command line: >cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff However, the job always failed with the following messages: NOTE1: Code tested with python 2.7.3.

Re: [gmx-users] Determining the cut offs more than half of the box

Dear Mr.Mark Abraham, Thank you for your help. Because of the accuracy of the results, I should use a reasonable cut offs for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too small for my project because of the importance of long range interactions. The box size is an

Re: [gmx-users] Determining the cut offs more than half of the box

Dear Mr.Mark Abraham, Thank you for your help. Because of the accuracy of the results, I should use a reasonable cut offs for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too small for my project because of the importance of long range interactions. The box size is an