[gmx-users] alchemical_analysis.py

HI GMX_users i am calculating free energy of ethanol following the tutorial from alchemistry website http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy i installed pymbar, and i also have script of alchemical_analysis.py (in the tutorial they have

[gmx-users] ligand.mol2

I've shared an item with you: ligand.mol2 https://drive.google.com/file/d/0BxaQk_pcR9viUmxfWXg2SmVJNFk/view?usp=sharing=CPef0EA=5684d0e3 It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] ligand.str

I've shared an item with you: ligand.str https://drive.google.com/file/d/0BxaQk_pcR9viTUhCc0w2YkMtbFk/view?usp=sharing=CK7LwfUJ=5684d110 It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] cgenff_charmm2gmx conversion error

Dear all, im trying to make itp file using cgenff_charmm2gmx.py i have given these comment python cgenff_charmm2gmx.py LIG ligand.mol2 ligand.str charmm36-jun2015.ff i got following error *NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used

[gmx-users] protonation_states

hi gmx users what should be the protonation states of of amino acids LYS, ARG, ASP, GLU, GLN and HIS at PH 2 Regards SSK -- 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] Problem in Free Energy Calculations

Hi Justin... I am following your Free Energy Calculations: Methane in Water tutorial. I am running it with the example files only. However I am little confused about some line written in it. It is written there : You should probably change the values of $FREE_ENERGY and $MDP, otherwise they

Re: [gmx-users] Calculate NMR shift from simulation

Hi Andrea, Thanks for your precious advice. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at

[gmx-users] temperature along the length of a box

Hi all, i have run a simulation of a 3x3x10 box for 20 ns. I would like to analyse the temperature along the length of this box. using g_traj just gave me the temperature of this whole box as a function of time. Could anyone know the way to have the temperature as a function of the box's length?

[gmx-users] Charmm gui error when making topology

Dear all, im trying to make topology for few ligands,(CHARMM ff)when i try to run it end with error i made unique name for all atoms using VMD-molfacature tool and used Discovery studio,open babel to convert to mol2 file for uploading to charmm-gui im getting following error awk: cmd. line:1:

Re: [gmx-users] Charmm gui error when making topology

On 12/30/15 9:21 AM, Nikhil Maroli wrote: Dear all, im trying to make topology for few ligands,(CHARMM ff)when i try to run it end with error i made unique name for all atoms using VMD-molfacature tool and used Discovery studio,open babel to convert to mol2 file for uploading to charmm-gui