[gmx-users] different versions- different output!

Hello all, I am a little confused since I am not getting the same output from the same input files using two different versions (the most recent one: 4.5.3 and 4.0.7). I am using two different machines and size of data generated from these simulations are not the same either. Below is the output o

[gmx-users] table-extension in mdp ?!

Dear users, Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the simulation with exactly the same input files but with version 4.0.7 and never got this error. Thanks for your comments.

[gmx-users] making index file

Hello, I am trying to make two different groups from residues below. one under the name Solute (residues a and b) and the other for solvent (residue c, SOL). The only way I know now is to do this by splitting the list of atom numbers [system] (default index file), from 1 to 362 and creating a new

[gmx-users] editying top file after solvation

Dear gmx users, I am solvating a solute with a solvent molecule using command line below: genbox -cp solute.gro -cs solvent.gro -o solvated.gro -p solute.top solute is in a 20nm cubic box and by this command I am getting solvated box. solute.top is the top file of solute. I searched the archive

[gmx-users] Treating nonbondend interactions in GROMACS

l. My understanding from reading the manual is that PME is for LR and switch and shift functions for SR. How could they be alternatives? Thank you, On 9 July 2010 20:15, Justin A. Lemkul wrote: > > > jojo J wrote: > >> Dear experts, >> >> I posted this message bef

[gmx-users] mdp file settings for PME

Dear experts, I posted this message before but I think you did not see it since I noticed messages after this have been replied. I have a hydrocarbon system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fou

[gmx-users] Ewald setting for hydrocarbon system?

Dear all, I need your favor. I have a hydrocarbon system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order =

Re: [gmx-users] top file

Hello, Thank you for your answer. I mean if I need to go back and comment those lines. (if the results are trusted ..actually I forgot to comment the lines..) On 8 July 2010 23:10, Justin A. Lemkul wrote: > > > jojo J wrote: > >> Helllo, >> >> I got top fi

[gmx-users] top file

Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Thank you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

[gmx-users] how to determine the box size

Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or longer than shortest di

[gmx-users] energy contributions / question about solvating

Hello everyone, I have a question on LJ and coulomb 1-4 energy terms. These are considered as intramolecular interactions and LJ and coulomb SR as intermolecular. If nrexcl in top file is 3, this means we obtain 1-4 energies, 1-5, 1-6, Now what we calculate as intermolecular (SR) contributions