Fw: [gmx-users] Energy minimization

  Sincerely, Shima - Forwarded Message - From: Shima Arasteh To: Dariush Mohammadyani Sent: Sunday, December 16, 2012 5:03 PM Subject: Re: [gmx-users] Energy minimization It's printed in terminal, exactly before showing the values of infinite potential and Max Force and .  

Re: [gmx-users] Energy minimization

It's printed in terminal, exactly before showing the values of infinite potential and Max Force and . Sincerely, Shima From: Dariush Mohammadyani To: Shima Arasteh Sent: Sunday, December 16, 2012 5:01 PM Subject: Re: [gmx-users] Energy minimization

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/16/12 12:52 AM, James Starlight wrote: Justin, It's not quite understood for me why such errors occurs in the atoms of standard residues when I've bounded them to the C term of my chromophore if the geometry of the adjacent residues might not be changed. So it likely that some errors occ

Re: [gmx-users] Re: Re: Is vacuum simulation NVT?

> Could you tell me is there any difference of different Tau_t ussage ( > inverse friction in case of Stochastic dynamics) for simulation of > water-soluble as well as membrane-proteins ? In the first case I'm > using tau_t 2ps that is lower than internal water friction. In the > second case one pa

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assig

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/16/12 10:34 AM, James Starlight wrote: Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? Probably something related t

Re: [gmx-users] gold-S simulation

Dear francesco I extract gold parameter from papers that I attached them for you. But  for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] gold-S simulation

hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you.   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] gold-S simulation

Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. I

[gmx-users] Box Pressure on individual box walls

Hello All, I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis. Thank you for your time. -- gmx-users mailing listgmx-users@gr

Re: [gmx-users] Box Pressure on individual box walls

On 2012-12-16 21:09, John Doe wrote: Hello All, I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis. g_energy will do it. Thank you for your time.

Re: [gmx-users] gold-S simulation

On 12/16/12 1:11 PM, francesco oteri wrote: Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and th

[gmx-users] Input vdwradii.dat file when using genbox

Dear All, I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the step "Solvate with water",i made a copy of vdwradii.dat and changed the value of C from 0.15 to 0.375. But i don't know how to input this changed file into genbox. I saw genbox -h, and i don't find any option for input

Re: [gmx-users] Input vdwradii.dat file when using genbox

On 12/16/12 10:15 PM, Kieu Thu Nguyen wrote: Dear All, I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the step "Solvate with water",i made a copy of vdwradii.dat and changed the value of C from 0.15 to 0.375. But i don't know how to input this changed file into genbox. I saw

Re: [gmx-users] Input vdwradii.dat file when using genbox

Thank Justin ! But i am not clear "Is it read automatically when i put it in the working directory or put it in $GMXLIB ?". The same question with gromos53a6_lipid.ff. To this new forefield, i put it in $GMXLIB as the tutorial said. Regards KT On Mon, Dec 17, 2012 at 10:17 AM, Justin Lemku

Re: [gmx-users] Input vdwradii.dat file when using genbox

I got it. Thank Justin ! Regards KT On Mon, Dec 17, 2012 at 10:28 AM, Kieu Thu Nguyen wrote: > Thank Justin ! > But i am not clear "Is it read automatically when i put it in the working > directory or put it in > > $GMXLIB ?". > > > > The same question with gromos53a6_lipid.ff. To this new foref

[gmx-users] oplsaa force field

Sir, I studying the dynamics of membrane proteins.First I did a 20 ns simulation using GROMOS96 53a6.This force field cause some problems in the helical part of the protein.Now I am trying to do the same simulation with opls-aa force field.Is the changes I should have to do in ffnonbonded.itp