[gmx-users] Generating a Log file from gmx hbond (5.1.4)

Hello, Have been trying all kinds of combinations to get gmx hbond to spit me out a .log file alongside my .xpm but nothings working. I've tried running: gmx hbond -f mtyhing.xtc -s mtyhing_eqpr1.tpr -n mtyhing.ndx -num mtyhing.xvg -g mtyhing.log -hbm mtyhing.xpm While everything else spits out

[gmx-users] problem about installing the latest version of MOPAC

In PDF manual (GROMACS_2016.4), it is mentiond. “ The current version of GROMACS provides interfaces to several popular Quantum Chemistry packages (MOPAC, GAMESS-UK ….. “ Please let me know if I missed anything. Thanks. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] dssp plot

Hi Dear all I used dssp plot to show the alteration of secondary structure for special residue numbers such as 100-200, but after calculation them, y axis of dssp plot is started from zero instead from 100. please let me know which part of m2p file should be changed to solve this problem. thanks

Re: [gmx-users] Fw: Potassium channel EM Segmentation fault

Thanks for Mark's prompt reply. I find there indeed are overlapping potassiums from each chain and I remove the extra potassiums then EM succeeds. Yu > -Original Messages- > From: "Mark Abraham" > Sent Time: 2017-10-11 22:12:29 (Wednesday) > To:

Re: [gmx-users] Fw: Potassium channel EM Segmentation fault

Hi, This is probably a case of http://www.gromacs.org/Documentation/Terminology/Blowing_Up and I suggest you consider some of the investigation approaches documented there. Mark On Wed, Oct 11, 2017 at 4:07 PM Du, Yu wrote: > > > > -Original Messages- > From:"Du, Yu"

[gmx-users] Fw: Potassium channel EM Segmentation fault

-Original Messages- From:"Du, Yu" Sent Time:2017-10-11 21:55:38 (Wednesday) To: GMX-user Cc: Subject: Potassium channel EM Segmentation fault Dear GMX Users, Keyword: metal, energy minimization, segmentation fault I

[gmx-users] Potassium channel EM Segmentation fault

Dear GMX Users, Keyword: metal, energy minimization, segmentation fault I have pinpointed the source of EM error. EM succeeds only without potassiums. I used PDB 1r3j and changed the TL to K. You can download the my 1r3j here and reproduce the error like this. $gmx pdb2gmx -f

Re: [gmx-users] Fwd: shift the LJ potential

I see, thanks Mark, Best regards On Wed, Oct 11, 2017 at 3:46 PM, Mark Abraham wrote: > Hi, > > To reproduce the training data for each forcefield, e.g. some experimental > or other computational result, e.g. the density of argon gas under various > conditions.

Re: [gmx-users] Fwd: shift the LJ potential

Hi, To reproduce the training data for each forcefield, e.g. some experimental or other computational result, e.g. the density of argon gas under various conditions. Details of what and how do vary with the force field, are are documented in its literature, of course. Mark On Wed, Oct 11, 2017

Re: [gmx-users] Fwd: shift the LJ potential

Apart from my own simulation, I do no understand how the values of C6 and C12 are obtained for each atoms in ''atometypes'' in force fields, could you tell me? Best regards On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett wrote: > > > On Wed, Oct 11, 2017 at 5:06 AM,

Re: [gmx-users] Fwd: shift the LJ potential

On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh wrote: > Thank you Wes and Mark, > > Wes, that is what I am trying to do. However, still have problem. > I do not know how to derive sigma, epsilon (or C6 and C12) for my particle? > How the force fields have obtained C6 and

Re: [gmx-users] Fwd: shift the LJ potential

Thank you Wes and Mark, Wes, that is what I am trying to do. However, still have problem. I do not know how to derive sigma, epsilon (or C6 and C12) for my particle? How the force fields have obtained C6 and C12 values in their .itp files for each atom? Best regards On Tue, Oct 10, 2017 at

[gmx-users] Topology file (type A type B format) for free energy calculation of bond breaking

Dear Gromacs Users I wish to calculate free energy simulation in which I wish to break bond within a molecule from state A to state B. If I use bond type 6 to define that bond in the molecule then i think it should not generate exclusions (as stated in the manual of Gromacs version 5.1.2,

[gmx-users] dihedral angle barrier height

Hi, I am a bit confused about the value that I should take as the dihedral angle barrier height. I am using Amber03 forcefield. What I can understand so far  from the ffbonded.itp file is that following are the parameters for psi and phi dihedral angles -  N   CT  C   N     9     180.0