[gmx-users] Persistence length of whole DNA molecule

Hi all, I want to calculate the persistence length of whole DNA molecule. I know that we can calculate it by using option g_polystat -f .trr -p p.xvg , but I am not able to figure out what set of of atoms I have to select while making the index, so that I could get persistence length

Re: [gmx-users] Persistence length calculation using g_polystat

, | | Am Fassberg 11, 37077 Goettingen, Germany | | Tel.: +49 551 201 2304| || On Sun, Jul 21, 2013 at 11:27 PM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Dear gmx users, I

[gmx-users] Persistence length calculation using g_polystat

Dear gmx users, I would like to calculate persistence length of DNA using gromacs command g_polystat . The out put file of persists.xvg contains persistence length in number of bonds and it shows that the average persistence length = 4.3 bonds. How can we convert no of

Re: [gmx-users] User-define non bonded table

Hi Neumann, You can use tabulated potential option in gromacs. Please check the site given below: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials Thanks, Mohan On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx

[gmx-users] How to choose bd_fric value in brownian dynamics

Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs.

Re: [gmx-users] How to choose bd_fric value in brownian dynamics

with? See manual for details of how this trick works. Dr. Vitaly Chaban On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein

Re: [gmx-users] surrounding a peptide by ions of magnesium

Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? Thanks, Mohan On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 12:38 AM, Mohan maruthi sena wrote: Hi all

[gmx-users] surrounding a peptide by ions of magnesium

Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we have 0.5 Molar Mg+2 solution, My question how

[gmx-users] elastic network model - atoms movement

Hi all, I want to build elastic network model using gromacs. I consider only c-alpha atoms and only bond stretching term contributes to towards potential energy. Bonds are connected between atoms present with in certain cut-off distance(modified topology accordingly). When I run md

[gmx-users] Elastic Network Model -harmonic pot

Hi all, I am trying to build an elastic network model using only C-alpha atoms . Potential energy function contains only bond stretching energy term rest like angle,dihedral and non bonded are not included. I use bond function type(f.tp = 6) ,i.e. is harmonic bond potential . The

Re: [gmx-users] Elastic network model

) with respect to elastic network model. Thank you, Mohan On Thu, Aug 30, 2012 at 5:58 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi , Thank you very much .I will take all these factors in to account while building the model. Thank you, Mohan. On Thu, Aug 30

[gmx-users] Elastic network model

Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

Re: [gmx-users] Elastic network model

are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model

Re: [gmx-users] Elastic network model

probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s

Re: [gmx-users] Elastic network model

Hi , Thank you very much .I will take all these factors in to account while building the model. Thank you, Mohan. On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 30/08/2012 10:17 PM, Mark Abraham wrote: On 30/08/2012 10:02 PM, mohan maruthi sena

Re: [gmx-users] Elastic network model -building

that are within a cut-off distance of your choice and then write a list of bonds that you could add to a gromacs topology file ... On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: Hi all, I want to build elastic network model for a protein. To build an Elastic network model

[gmx-users] Elastic network model -building

Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do

[gmx-users] Topology- make bonds with certain cut-off distance

Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Topology- make bonds with certain cut-off distance

that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing. Erik 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: Hi all, I

[gmx-users] Elastic network model -gromacs

Hi all , Can any one suggest me how to build elastic network model in gromacs ( any literature,tutorial kind). Thanks in advance, K.Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed!

[gmx-users] elastic network model -protein contracting

Hi all, I want to prepare a basic elastic network model (tirion model) of protein. For this i have taken only C-alpha atoms of the protein and considered only streching potential(k.(b-b0)^2)) and removed rest of angle,dihedral,non bonded interactions. I have mentioned a bond

[gmx-users] Create a elastic network model -attach a spring between to atoms with force constant

Hi all, I want to create an elastic network model for a protein, in which i have selected only c-alpha atoms(removed rest of the atoms). To attach a spring between alpha atoms with some force(spring) constant k , How can i mention this in topology file ? Thanks, Mohan --

[gmx-users] Tabulated potential 1-4 interactions

Hi all, I am using tabulated potential option for non bonded interactions. The system that i am using contains on CA(alpha) CB(beta) ,atoms connected, If i use option energygrps = CA CB energytable = CA CA CB CB it caluclates potential between

[gmx-users] unable to generate gro file -(only c alpha atoms -named as CB)

Hi all, My pdb file contains only c-alpha atoms , i have named alternate CA atoms(res) as CB(1res CA,2res CB,3res CA...) , I have given my residue name as ALB, accordingly i have changed .rtp ,atomtype files,residuetype.dat. i want to use force field(charmm27.ff) present in current

[gmx-users] repulsive interaction i and i+2

Hi all, I have used a user define potential to describe attractive potential beyond i and i+3 atoms(similar to lLJ). If i want to describe repulsive interactions with in i and i+3 , how can i do it in gromacs? can anyone suggest me a way, Thanks and Regards, Mohan -- gmx-users mailing

[gmx-users] bonded interactions as table

Hi all, I have learned from manual that non bonded interactions can be given as user defined potential by using tables. If i want to give dihedral term as user defined potential keeping rest of the bonded parameters in their usual form, how can i do that. Please suggest me a way,

[gmx-users] user defined potential(repulsive) for atoms falling with in three residues

Hi all, I am using a user defined potential to describe non-bonded interactions, which describes attractive potential for residues separated by four or more bonds . Now I want to describe a user defined potential(repulsive) for atoms falling with in three residues and which are not

[gmx-users] How can i specify a user defined potential between i, i+2 residues

Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. T -- gmx-users mailing list

[gmx-users] Fwd: How can i specify a user defined potential between i, i+2 residues

Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Thanks for a reply in

[gmx-users] User defined potential

Hi all, I want to define a potential form and give it as input for which i have seen manual ,thought gromacs table option is fine, i have an example of generating 9-6 potential form , My question is how to generate table.xvg, what is the command to generate table.xvg from code table.c.

[gmx-users] Go model -error in generating topology

Hi all, I try to build go model(which uses only c-alpha atoms), my pdb contains only c-alpha atoms extracted from the original pdb file ,when i use pdb2gmx command on c-alpha containing pdb file it gives the following error. Atom N is used in an interaction of type atom in

[gmx-users] error in oscillation period

Hello everyone, I am getting the following error when i execute grompp command ,can anyone please explain me why this error arises, *NOTE 2 [file ile.top, line 2986]: The bond in molecule-type Protein_chain_I between atoms 22 N and 23 HN has an estimated