Re: [gmx-users] LJ potential

Be careful if you are going to change the parameter to zero , because there is a combination rule that defines the usage of C6 and C12. and this combination rule is defined in the *.itp file On Mon, Sep 27, 2010 at 8:34 PM, nishap.pa...@utoronto.ca wrote: How can I do that using OPLSAA, because

[gmx-users] fudgeLJ and fudgeQQ setting in the *.itp file

Hi All, I was just wondering whether someone knows what are the considerations in choosing the values for* fudgeLJ* and *fudgeQQ* in the [defaults] section of the *.itp file. (these two factors multiply the 1-4 LJ interactions and the electrostatic interactions , respectively) the manual

[gmx-users] [nonbond_params] section , choice of parameters

Hi All, I want to exclude attractive Lennard-Jones interactions between atoms that i defined in the ffamber99nb.itp file. the properties of the dummy atom which I defined are: *amber99_69X 0. 0. A 3.39967e-01 3.59824e-02* ; (i.e., Sigma=3.39967e-01 and

Re: [gmx-users] RE: [nonbond_params] section , choice of parameters

Hi Ehud, Did you mean that i can simply specify Sigma and Epsilon? The thing is that i didn't want to obtain a zero potential , but rather maintain the repulsive term of the LJ interaction. What would you specify then, for the C6 and C12 parameters? Amir On Wed, Jul 28, 2010 at 3:00 PM, Ehud

Re: [gmx-users] RE: RE: [nonbond_params] section , choice of parameters

Many Thanks Ehud! I was certainly not aware of that and I'll check it now.. Amir On Wed, Jul 28, 2010 at 6:22 PM, Ehud Schreiber schr...@compugen.co.ilwrote: Hi again, Yes, you can simply specify sigma and epsilon, but indeed in your case you do not want to do so but rather to specify

[gmx-users] energygrps and simulation run time

Hi, Does the use of energy groups (energygrps) in the *.mdp file may cause some slow down in the simulation running time? Thanks, Amir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] nonbond_params

Hi, my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon) I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms , such that only the repulsive terms

Re: [gmx-users] nonbond_params

: Amir Marcovitz wrote: Hi, my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon) I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms

[gmx-users] Units of the Amber99 parameters

Hi All, sorry for the naive question, but perhaps someone can tell me what are the units of the VDW parameters (i.e., Sigma and Epsilon of the Lennard-Jones potential) in Amber force-field? (I'm not sure if its kjoul/mol or kcal/mol) Thanks, amir -- gmx-users mailing list

Re: [gmx-users] output of the -hist option of the g_wham command

Hi, It simply gives you the histogram of each individual input simulation for the umbrella. From my experience, it is very useful in cases that you're WHAM will not converge and it allows you to verify weather there is a sufficient overlap between adjacent input configurations.It can be useful in

Re: [gmx-users] error in parallel mdrun

Hi Gavin, I had exactly the same problem a few days ago. you have 2 options for parallel runs: domain decomposition (default) and particle decomposition you can either try to manipulate the parameters of your system such that they fit domain decomposition or choose the easier way..that is using

[gmx-users] A confusion about domain decomposition

Hi all, I'm trying to run a parallel Job for a system of dummy atoms that arranged as 2 surface (each is 6X6 atom surface- with bonds that i defined between them) the system is solvated in a box of dimensions 4.5nm X 6.5nm X 4.5nm with salt, minimized and equlibrated fine. however, when trying

Re: [gmx-users] g_wham gets stuck

wrote: Justin A. Lemkul wrote: Amir Marcovitz wrote: Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs

Re: [gmx-users] g_wham gets stuck

, Thanks a lot for the quick reply Amir On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub joc...@xray.bmc.uu.se wrote: Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF

[gmx-users] g_wham gets stuck

Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all

Re: [gmx-users] value of an angle

Hi, if you are interested in a particular angle (between a triad of atoms) you can specify it in angle.ndx file (to generate the angles run: mk_angndx -s topol.tpr -n angle.ndx) the -ov flag of g_angle will generate the angle trajectory and the -od flag will generate its distribution cheers On

[gmx-users] bonds section in the topology file

Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar for that

Re: [gmx-users] bonds section in the topology file

for my previous post) do you think bond type 6 will settle this? anyway, thanks a lot for the quick reply! Amir On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amir Marcovitz wrote: Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms

[gmx-users] Restrict rotation between 2 molecules

Hi, i want to simulate 2 parallel plates (each composed of single atoms with equal spacing , for example 2X2 atoms plate) i want to simulate them such that they are parallel to each other and can move only along one axis (for that i used posre.itp..) what is the best best way to prevent them

[gmx-users] Fwd: mdrun error

-- Forwarded message -- From: Amir Marcovitz amarcov...@gmail.com Date: Mon, Jan 4, 2010 at 6:18 PM Subject: mdrun error To: gmx-users-requ...@gromacs.org Hi, my system is composed of 2 molecules that are arranged in a lattice: i.e., each molecule is represented by 4 atoms

Re: [gmx-users] Problems with umbrella sampling

apply for the WHAM analysis after the run? thanks, Amir On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amir Marcovitz wrote: Hi, my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one

[gmx-users] Problems with umbrella sampling

Hi, my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one of them (SRP) and negatively charged on the other plate (SRN). i want to perform a simulation with umbrella sampling between the 2 so i defined the pulling

Re: [gmx-users] Adding ions

Hi, Make sure you do specify the explicit names of the topology and structure file. in the mannual they omit the suffix of the file. for the purpose of rigourism - this is the line i'm using: genion -pname Na+ -nname Cl- -o file_ionized.gro -conc 0.2 -p topol.top On Tue, Nov 17,