[gmx-users] genion question

Hi Dear Gromacs Users, I have a doubt , if i need a electrolyte concentration of 150mM of ions of NA and CL the right comand is genion -s file.tpr -o topol.top -nname CL -pname NA -neutral -conc 0.150 -o out.gro ? thanks in advance -- Gromacs Users mailing list * Please search the archive

[gmx-users] Re gromacs Bug?

Thank You Justin , i will check with gmxdump, thank you -- 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 * For (un)subscribe requests visit

[gmx-users] g_wham tpr files

Hi Dear Gromacs Users, I ran a US simulations but i checked my .mdp file, i put the pull_coord1_vec = 0.0 0.0 1.0 ; instead of pull_coord1_vec = 0.0 0.0 -1.0 ; (the correct one) it is ok to use grompp and generate the right .tpr files, and use the pullf-files that i already have and

[gmx-users] Help Energy Diferences

Hi Dear Gromacs Users, I have been dealing with a problem, i run an MD of my sistem , and i see problems with my energies due to one of my molecules is a CNT and has no charges and its Coul SR are huge, well i though this could be of an error in my NDX file , the thing is that i run my MD in my

Re: [gmx-users] Help Energy Diferences

Hi i run again the MD, but wtih MD mdrun -nb cpu, in order to check , and the energy make sense now, how can i get the correct use of Gromacs with GPU? i compile it with cuda, and the program recognize the GPU -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Re gromacs Bug?

Hi Justin , i thought the same as you, that the problem is with the NDX file, but i check the selection, the file and made diferente gro files, in order to check the atoms, and there are ok , or fine , Andrés Ortega -- Gromacs Users mailing list * Please search the archive at

[gmx-users] energy help

Hi dear gromacs Users I am dealing with a Coul SR energy problem, my system has an CNT , Water, Ions , POPC and an ION CHANNEL, i have already equilibrating, the Temperature and Pressure are OK, but when i run 10ns of MD, my Coul SR CNT-CNT is really big, Energy

[gmx-users] gromacs Bug?

Hi dear Gromacs users, i would like to report something maybe could be a bug or a mistake of me , you´ll see, i run an MD of a System with CNT Protein Water and ions, i use a index.ndx file, my CNT doestn´t have any charges, but when i check the Coul SR CNT-CNT there were really huge, so i start

[gmx-users] g_wham -sym question

hi dear Gromacs User, i was wondering if you could help me with something, I made a set of Umbrella sampling simulation of a Drug passing through a POPC membrane, i use Gromacs 5.0 rc1, i use the geometry direction , when i use g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -ac

Re: [gmx-users] g_energy help

Thank you Justin ,for the help , but i really dont get it, energy tyoe CNT-CNT mean within ? , you mean inside? or al the energy that the CNT is experiment by the nonbonds of itself? thank you -- Gromacs Users mailing list * Please search the archive at

[gmx-users] g_energy help

Hi dear Gromacs User , i was wondering if one of you could help me with something i use genergygroups to molecules of my system CNT PROTEIN so when i use g_energy i can see two types of interaction like Coulomb and LJ, What does mean CNT-CNT and CNT-rest interaction? or PROTEIN-PROTEIN,

Re: [gmx-users] CNT ROTATION

Should i try instead different pull MD(changing the pbcatom, CNT's COM, velocity,force) , in order to get new configuration for an umbrella sampling simulation and a PMF in z Axis calculation, until i´ll get no rotation in the CNT? or can i used this MD, to get the configuration for the Umbrella

Re: [gmx-users] Diferent Pressure Solvent

I have this idea to try to emulate a chemical gradient, this is because i would like to see the diffusion of a molecule that it is caged in the SWCNT, an see if i can reproduce a chemical gradient in order to see a diffusion of the molecule, This idea is to try to model a chemical gradient

Re: [gmx-users] Diferent Pressure Solvent

I would like to aplied a force like in this paper, but with gromacs Pressure-Induced Water Transport in Membrane Channels Studied by Molecular Dynamics Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten -- Gromacs Users mailing list * Please search the archive at

[gmx-users] CNT ROTATION

Hi Dr Vitaly , First 3nm it is not half of any side, i used the external amino acids from the channel as a reference gruop, and 3nm is the distance from the SWCNT tip's to the channel, but 6nm from the COM, my box has 19 nm in Z axis, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Diferent Pressure Solvent

Hi Dear Gromacs Users I was wondering if i want to simulate a SWCNT with water inside, it possible , to run an MD with the inside water with a diffent pressure (2 Bar) , and the outside water and CNT a 1 bar?, It is ok to use an index file, and use different pressure values with the barostat i

[gmx-users] CNT ROTATION

Hi dear Gromacs User, I have done a pulling simulation of a SWCNT against an ion channel(the SWCNT , and the ion channel pore's are the same), in order to study the interaction between SWCNT and the outside (extracellular side) of the channel, So i put the SWCNT about 3nm of distance from the ion

[gmx-users] flat-bottomed potentials

Hi Dear Gromacs Users, I am running a umbrella samplimg simulation with gromacs 4.6.5, this simulations is a molecule permeating an ion channel, i decided to use X Y position restraints 400KJ , but i am not pretty sure if this kind of bias if a real mistake, i was wondering if anyone know how to