[gmx-users] RV: About Deuterium order parameters

Hello gromacs users: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way: > a C34 > a C36 > a C37 > a C38

Re: [gmx-users] Trr file not generated

On 11/6/16 8:21 PM, Mishelle Oña wrote: Hello! I made a relaxation md simulation with the parameters attached above and in the output there is no .trr file generated. Am I forgetting something in my mdp file?

[gmx-users] Constant force

Dear Justin Lemkul,which parameter exactly introduced constant force in during simulation? exactly in during simulation. it is "pull_coord1_k       = 1000 " ? Many thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] "C compiler accepts -mavx512f... no" (error compiling)

Hi, The fftw auto download now uses the new 3.3.5 version, which supports avx512 SIMD, but I guess they and we haven't tested the aspect of whether it's configure by works with gcc that is too old. To work around, you can build fftw yourself, or use one from your distro, or use a newer gcc

[gmx-users] binding free energy with gromacs2016

Dear users, I will try to do binding free energy calculation using GROMACS2016 but I am confused a little bit about the preparation of the input files. I have a few questions: 1) There are below lines to apply a harmonic distance restraint in the mdp files of the binding free energy tutorial

[gmx-users] About Deuterium order parameters

Hello gromacs user: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way: > a C34 > a C36 > a C37 > a

Re: [gmx-users] "C compiler accepts -mavx512f... no" (error compiling)

On 11/6/16 3:11 PM, Jacob Nowatzke wrote: I've installed GROMACS 2016.1 on my laptop and it works splendidly. When I install on my desktop, however, it does not. On the desktop I use: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=ON When I make

[gmx-users] "C compiler accepts -mavx512f... no" (error compiling)

I've installed GROMACS 2016.1 on my laptop and it works splendidly. When I install on my desktop, however, it does not. On the desktop I use: >cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=ON When I make check, it stops short and gives: checking

Re: [gmx-users] GROMACS-5.1.4 vs. GROMACS-5.1.2

On 11/6/16 12:31 PM, amitbe...@chemeng.iisc.ernet.in wrote: Hello Everyone, I was initially using GROMACS-5.1.2. But in my institute cluster they have recently installed GROMACS-5.1.4. I just wanted to know will there be any difference in result between these two versions. Sure, but patch

[gmx-users] GROMACS-5.1.4 vs. GROMACS-5.1.2

Hello Everyone, I was initially using GROMACS-5.1.2. But in my institute cluster they have recently installed GROMACS-5.1.4. I just wanted to know will there be any difference in result between these two versions. Regards, Amit Behera -- This message has been scanned for viruses and dangerous

Re: [gmx-users] Questions about free energy calculation tutorial

On 11/6/16 10:44 AM, gozde ergin wrote: This may be unstable, and is generally not done. Turn off charges linearly, then turn off LJ with a soft-core potential (or vice versa). The point is you should never have charges on atoms with no (or drastically reduced) LJ terms. This can be easily

Re: [gmx-users] Questions about free energy calculation tutorial

> This may be unstable, and is generally not done. Turn off charges linearly, > then turn off LJ with a soft-core potential (or vice versa). The point is > you should never have charges on atoms with no (or drastically reduced) LJ > terms. This can be easily specified in an appropriate

Re: [gmx-users] Questions about free energy calculation tutorial

On 11/6/16 8:27 AM, gozde ergin wrote: If it's the salt, then take the known Na+ value for the force field and add it to the SDS value you obtain at infinite dilution. Straightforward. Ok either I can take hydration free energy of Na from the literature or I can run 2 thermodynamic

Re: [gmx-users] Questions about free energy calculation tutorial

> If it's the salt, then take the known Na+ value for the force field and add > it to the SDS value you obtain at infinite dilution. Straightforward. Ok either I can take hydration free energy of Na from the literature or I can run 2 thermodynamic integration with dodecyl sulfate and Na

Re: [gmx-users] Questions about free energy calculation tutorial

On 11/6/16 7:38 AM, gozde ergin wrote: If you need the total free energy of hydration for NaSDS, you can just decouple SDS in water with no Na+ and sum the two contributions (SDS and Na+ separately). If you just want the SDS hydration free energy, decouple it in a box of pure water

Re: [gmx-users] Questions about free energy calculation tutorial

> If you need the total free energy of hydration for NaSDS, you can just > decouple SDS in water with no Na+ and sum the two contributions (SDS and Na+ > separately). If you just want the SDS hydration free energy, decouple it in > a box of pure water Thanks Justin, I have difficulty to

Re: [gmx-users] Umbrella sampling

On 11/6/16 1:53 AM, m g wrote: Dear Justin, In umbrella sampling tutorial, what force constant was used during the umbrella sampling simulations? Please read the contents of the .mdp files provided in the tutorial. -Justin -- == Justin A.

Re: [gmx-users] Questions about free energy calculation tutorial

On 11/5/16 11:51 AM, Alex wrote: Hi, Concerning to the Na+ charge, if we were interested in the relative binding free energy in a system (\Delta\Delta G), I mean the difference between two Free energy in the Ligand and Complex situations, then could you please confirm me that you can make

[gmx-users] Umbrella sampling

Dear Justin, In umbrella sampling tutorial, what force constant was used during the umbrella sampling simulations? Many thanks, Mr. Ganj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?