Re: [gmx-users] run MD in vacuum

This settings work, but version isn't newest. integrator<>=<->md dt<><-->=<->0.001 nsteps<><-->=<->1010 nstxout><-->=<->1 nstcalcenergy<->=<->100 nstenergy<->=<->100 cutoff-scheme<->=<->group pbc<--->=<->no nstlist>=<->0

[gmx-users] Entropic effects in PMF at zero distance

The formula (5.283) from PDF manual or (3) in http://manual.gromacs.org/documentation/current/reference-manual/special/free-energy-implementation.html#potential-of-mean-force   V(r)=-(n-1)*kT*log(r) is obviously incorrect at r=0 for non singular potential (f.e. if "r" is the distance between

Re: [gmx-users] Obtaining opls forcefield

oplsaa force field is situated in /usr/share/gromacs/top (on my PC) folder in gromacs format. If you want to generate oplsaa topology for non-protein molecule it is very comfortable to use acpype (git clone https://github.com/alanwilter/acpype.git) or Jorgensen server

Re: [gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?

pdb2gmx isn't acceptable for any molecule. Only for proteins and DNA-RNA. β-cyclodextrin is present in atb.uq.edu.au in many variants for force field G54A7FF Or it is quit simple to build β-CD with glycan builder and modeller from charrm-gui.org (7 times connect α glucose with 1-4 link). One

[gmx-users] Changing mdp options for a restart

http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart   I tried to simulate instantaneous perturbation in topology and did everything as in instruction (below). Changing mdp options for a restart If you wish to make changes to

Re: [gmx-users] QMMM with GROMACS and DFTB3

It seems that ORCA compatible with latest GROMACS if I correctly understand meaning of "//". Look in  CMakeCache.txt file in the installer. //QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess, // orca GMX_QMMM_PROGRAM:STRING=None -- Gromacs Users mailing list * Please search

Re: [gmx-users] QMMM with GROMACS and DFTB3

Im am also starting to perform QM/MM in GROMACS for dyes in ground and excited states in supramolecules, but didn't decided yet what QM package (MOPAC, ORCA or GAMESS-US) will be. But aware of calculation speed of DFT QM in non-empirical methods for average-size molecules I suppose that needed

Re: [gmx-users] QMMM with GROMACS and DFTB3

http://wwwuser.gwdg.de/~ggroenh/qmmm.html   or 8.13.1 ORCA and Gromacs chapter in orca4 manual. What will be the speed of calculation? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Solid state barostat

I am trying to simulate amorphous organic solid system with Parrinello-Rahman at P=1 Bar. The maximal dt value which holds molecules together is 0.0008 and it's increasing leads to evaporation. What may be incorrect? Berendsen works well with dt=0.001 but it isn't recommended. mdp options for

[gmx-users] the energy of the individual molecule

Suppose the trajectory of molecular system with interactions between all molecules. How is to obtain the time dependence of intramolecular energy of the given molecule with unique resname and the total energy of this molecule in the system including intermolecular interactions? -- Gromacs

Re: [gmx-users] topology for excited electronic state

I found an answer for my old question in amber tools. As it is possible to input the electronic multiplicity in antechamber with "-m" option, the topology for excited electronic state can be produced in the case then the necessary state has different multiplicity than the ground one. --

Re: [gmx-users] Does GROMACS write charges?

> >No, because that would be a waste of disk space. Charges are a fixed Then "gmx dipoles" will be incorrect in the analisys of the simulation with variable   charges. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Does GROMACS write charges?

Does GROMACS write atomic charges in "trr" or "edr" files during trajectory calculation? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

Re: [gmx-users] Charges in alchemistry

Of course "free-energy =   yes" is written in mdp-file. I didn't notice to paste it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] selections

Greetings. Please help to solve simple task with gromacs selections. Say, I have the box with 1000 identical molecules. How to output the array of "nearest neigbours" (for example by distance between COM <5 Angstroms) for each molecule in the box at the time moment=T. -- Gromacs Users mailing

Re: [gmx-users] lambda value for free energy calculation

>when should we consider temperature_lambdas, mass_lambdas,restraint_lambdas? If hamiltonian of the system changes between initial and final states the corresponding part is given in coul-lambdas vdw-lambdas bonded-lambdas restraint-lambdas mass-lambdas temperature-lambdas change the external

Re: [gmx-users] Force field informations

>I would like to know where we would get the force field information in GMX The answer is obvious: read manual (chapter 4 I"nteraction function and force fields" and 4.10 "Force field"). The FF files are situated in /usr/share/gromacs/top (for my PC) and are transparent enouth. -- Gromacs

Re: [gmx-users] hydration free energy

| Have you tried other FE estimate algorithms (i.e. thermodynamic >integration, MBAR, etc.). Look into the project "alchemical-analysis". It's >a python script that will give you some good visualizations on what is >happening at that last step (it's compatible with GROMACS output files). >There's

Re: [gmx-users] hydration free energy

>If there are no vdW and Coul it still calculates the average energy, which >without soft-core technique can be very large when atoms overlap. >You can read >http://www.sciencedirect.com/science/article/pii/S0010465516303411 Eq. (2) and >the following text etc.  >You can try a soft-core

Re: [gmx-users] hydration free energy

Hi, > >Do you know which values of lambdas are used? >Are you using a soft-core technique? > >Asaf Thanks for discussion. I am waiting already few days for anyfing reply. The technique of calculation in the file job.sh. The value of coul- λ is uniformely increasing from 0 to 1 with the step 0.02

[gmx-users] hydration free energy

Hi. I have calculated deltaG of hydration for my molecule in 101 steps. First 50 steps I decoupled coulomb interactions and last 50 - vdw. After all I calculated resulting value by the command gmx bar -f {0..100}/dhdl.xvg -o -oi -oh -b 500 >RESULT and found such phrase in the output

[gmx-users] topology for exited electronic state

It is well documented how to construct topologies for ground states of molecules and ions. My task is to simulate the behaviour of dye (anion) after laser exitation in supramolecular complex. Is it possible with standard gromacs force fields? -- Gromacs Users mailing list * Please search the

[gmx-users] gmx velacc

Hi. This is my first letter to this list, sorry. version:  :-) GROMACS - gmx help, 2016.4 (-: Problem with velacc command ( http://manual.gromacs.org/documentation/2016.4/onlinehelp/gmx-velacc.html  ). In the folder with calculated long trajectory I input: gmx velacc -f traj.trr -mol -b 10 -e 20