Re: [gmx-users] question about make_ndx

Hi, Under Unix/Linux you can use gmx make_ndx -f struc.gro -o test.ndx << _EOR_ r 1 q _EOR_ Best, Thomas. -- R. Thomas Ullmann, PhD Theoretical & Computational Biophysics Max

[gmx-users] Functional Mode Analysis (FMA)

Hi Eduardo, The FMA tool is not yet included in the official distributed GROMACS version, but it is under code review. You can build GROMACS with the FMA tool from the attached tar ball of the development version that is currently being reviewed. The FMA tool can then be called as gmx fma

Re: [gmx-users] Binding cavity analysis

Hi, I forwarded your email to the GROMACS users list, please use it for user questions. In this way you have a greater chance of getting answers and others can find the questions and answers online. >I have a 2 microsecond trajectory of protein-ligand system. I want to >calculate 3 things: >

[gmx-users] FW: Binding cavity analysis

From: Wycliffe Omwansu [womwa...@gmail.com] Sent: Saturday, August 11, 2018 7:29 AM To: Ullmann, Thomas Subject: Binding cavity analysis Hi, I have a 2 microsecond trajectory of protein-ligand system. I want to calculate 3 things: 1. Time series of number

Re: [gmx-users] Any update on constant pH simulation?

Hi Jagannath, The current implementation an older GROMACS version (3.3.1) can in principle be used, but is slow for systems with many titratable sites na d has some other restrictions. You find it here: http://www.mpibpc.mpg.de/grubmueller/constpH The new constant pH framework will offer

Re: [gmx-users] fe4s4

A good starting point to get an idea of the challenges posed by iron sulfur clusters are the publications of Louis Noodleman. Good luck, Thomas. -- R. Thomas Ullmann, PhD

Re: [gmx-users] Nitrate parameters CHARMM

Hi Tyler, http://dx.doi.org/10.1002/smll.201102056 Best, Thomas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tyler Cropley [tyler.crop...@wagner.edu] Sent: Thursday, February

Re: [gmx-users] trjcat

Hi Elham, use trjconv -dt NEW_TIME_STEP_IN_ps. Happy simulating, Thomas. -- R. Thomas Ullmann, PhD Theoretical & Computational Biophysics Max Planck Institute for Biophysical

Re: [gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series

For the record, the problem of not getting the output expected from gmx distance may have been related to a bug fixed here: https://gerrit.gromacs.org/#/c/4843/1 Happy computing, Thomas.

Re: [gmx-users] short-range eletrostatic energy of every aminoacid

Hi Diogo, create an index file, either with gmx select or gmx make_ndx, and feed it to grompp. Happy computing, Thomas. -- R. Thomas Ullmann, PhD Theoretical Computational

Re: [gmx-users] PCA of crystal structures

Hi, you can directly project the crystal structures onto the eigenvectors from the PCA with gmx anaeig. It may be necessary to create an index file for each PDB file with an index group that identifies the atoms that correspond to the vector components. Make sure that the order of atoms is the

Re: [gmx-users] All atom MD Simulation

Can we analyse catalytic mechanism of an enzyme using the classical all atom MD simulation. No. I would say, that is a bit too pessimistic and unnecessarily demotivating. You can not directly simulate the catalytic reaction without employing a quantum chemical treatment (or a reactive force

Re: [gmx-users] Constant pH simulations

Hi, Not yet, but we are working on it. Best, Thomas. -- R. Thomas Ullmann, PhD Theoretical Computational Biophysics Max Planck Institute for Biophysical Chemistry Am