[gmx-users] how to set temperature-lambdas

Dear users, I am confused about setting "temperature-lambdas" for free energy calculations. I use a total of 15 lambda windows. In the mdp file, the temperature should be 450 K at lambda = 0.5 and it symmetrically should go to 300 K at both end states lambda=0 and lambda=1. For this aim how

[gmx-users] REMD

Hello GROMACS users, As far as I understand, increasing the number of random exchanges to a large number (mdrun suggests N^3 where N is the number of replicas) moves a REMD simulation from a neighbor exchange procedure to a Gibbs exchange procedure. Can anyone provide some practical advice or

[gmx-users] Gromacs do oscillatory shear/box deformation?

Greetings gromacs community I've be thinking at looking at some viscoelastic properties and was hoping to avoid the slow convergence of the green-kubo method and use NEMD methods; however, from the manual I can't tell if the deformation options in for the mdp file are oscillatory or constant.

Re: [gmx-users] Unable to make install Gromacs on Cygwin

On 8 June 2018 at 19:35, Matthew Fisher wrote: > Hi there, > > > I'm wondering if anyone could help me. I've been compiling GROMACS in > Windows using CYGWIN and this tutorial - http://megaddl.pcriot.com/ > installing-gromacs-5-1-1-in-windows-using-cygwin/ > > However, when I go to make install,

[gmx-users] Unable to make install Gromacs on Cygwin

Hi there, I'm wondering if anyone could help me. I've been compiling GROMACS in Windows using CYGWIN and this tutorial - http://megaddl.pcriot.com/installing-gromacs-5-1-1-in-windows-using-cygwin/ However, when I go to make install, I get the following output: $ make install [ 0%] Built

[gmx-users] Problem with freeze groups

Hi gromacs users again, I have a problem with freezing of the atoms in my simulations. I have prepared kaolinite surface and have tried to run NVT simulation (see attached mdp file) with frozen outer layers (BULK section in my index file). I run it with GPU. While in 2016.5 version everything

[gmx-users] Handling PBC for Free energy calculations in plumed patched Gromacs

Dear all, I am trying to study free energy profiles for base flipping in a DNA+Protein system via umbrella sampling calculations on Gromacs 2016.3 patched with PLUMED 2.4.1. On visualizing the GRO file which comes after equilibriation (and which is used to make the initial TPR that each window

Re: [gmx-users] Regarding rigidity of water models

Hi, [1] CHARMM36 is to be used with the CHARMM-modified TIP3P water model (TIP3P with LJ parameters on the water molecule hydrogen atoms). [2] By default it's rigid, but check "define =" under your mdout.mdp file. If there's no -DFLEXIBLE, then it's rigid. [3] No idea of what that is, sorry.

[gmx-users] Regarding rigidity of water models

Hello all, I have done a simulation with amino-aid+cosolvent+water in which for the amino-acid and co-solvent i have used charmm36 FF and SPC model for water. I have a few Doubts:- 1) Is this SPC water model which i have used is suitable in case of charmm36ff..?? Referring to Justin's answer in

Re: [gmx-users] Rupture force definition

Dear Justin . I have two query 1-What can be the optimized value of rate can be taken for pulling of dsDNA/dsRNA using gromacs format where solvent is aqua. >From your umbrella sampling manual, rate is very high like (0.01 nm/ps), which is equal to 0.0001Angstrom/fs. 2- In pulling mdp file