Re: [gmx-users] help---How to define new residue in GROMACS?

?? wrote: My problem is How to define new residue in GROMACS? i have made a 3-d structure model for a protein based on a template protein??which has a heme group. befor runing the gromacs molecular simulation,i must define the heme group as a new residue,How to define new residue in

Re: [gmx-users] g_wham problem

Oh, that would be convenient.   Thanks.   --- 09年8月3日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] g_wham problem 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年8月3日,周一,上午9:01 accomp lin wrote:   Dear all  

[gmx-users] Fwd: help-how to define a new residue in gromacs ?

This is what the GMX user list is for. Please post such requests there. Tsjerk -- Forwarded message -- From: 郭建路 zimoguojia...@163.com Date: 2009/8/4 Subject: help-how to define a new residue in gromacs ? To: tsjerkw tsje...@gmail.com HI Tsjerk: can you help me ? My problem

[gmx-users] query about simulation of a protein containg a metal ion

Dear Sir,          I want to simulate a protein with a CA2+ ion and one crystal water using G431 force field, simulation of the protein without the metal ion went off successfully,But while running the simulation with the metal ion it's giving  a fatal error during position restrained

Re: [gmx-users] reg mopac gromacs installation

dear Mark Abraham  sir,  pardon  for the disturbence through mail thank you for your atonce reply herafter i will contact u throug the gmx mailing list. please sorry for the inconvience. i am in budding stage  in gromacs MD research      --- On Tue,

RE: [gmx-users] FudgeLJ

No, you can not use pair parameter generation at all with Buckingham, since 1-4 interactions are always LJ and you can not convert Buckingham to LJ parameters. Unfortunately Gromacs 4.0 does not check for gen-pairs=yes, Gromacs 4.1 will give a fatal error when you turn it on. Dispersion

[gmx-users] g_vanhove output

Hi all, I believe there is a mistake in g_vanhove in version 4.0.5 The 'xvg' output file labels the y axis as G, with nm^-1 as units. From the units, I guessed that the output was actually r^2 G, however the initial slope is linear and not quadratic. After a few tries I concluded that the

RE: [gmx-users] g_vanhove output

Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference

Re: [gmx-users] g_vanhove output

Thanks Berk. I did look at the code, but it is not that easy to understand. My conclusion comes from this: for a diffusive regime, G(r) should be a gaussian function, with the diffusion coefficient characterizing the width. I did some tests, and I could match both curves (one from g_vanhove

Re: [gmx-users] query about simulation of a protein containg a metal ion

sangeeta kundu wrote: a) Temperature coupling groups must include all atoms in the system. Do not couple handfuls of atoms separately. So Protein and Non-Protein are often right. b) If you use -n you need to supply an index file, which you might make with make_ndx. That index file must

Re: [gmx-users] 1-4 interaction at distance larger than 1

Thank you very much, yes normally, the header of pdb file has remark 465 and 470. I just used the modeller loop to add the missing residues according to remark 470, and did not add following remark 465, is it right? because there are only RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE

Re: [gmx-users] 1-4 interaction at distance larger than 1

Yi Hou wrote: Thank you very much, yes normally, the header of pdb file has remark 465 and 470. I just used the modeller loop to add the missing residues according to remark 470, and did not add following remark 465, is it right? because Normally one has to deal with *both* missing residues

[gmx-users] Different force field: Gromacs vs Autodock

Hi I use Gromacs (ffG45a3) to run MD in the protein vs ligand system. Then, I use Autodock to calculate the protein-ligand binding energy. As I know the force fields are different between ffG45a3 and Autodock. The two different force fields explain the same system. How can I explain this?

RE: [gmx-users] g_vanhove output

I think I coded this all correctly, but the last time I used it was years ago. In 3D you could plot G(x), G1(y) and G(z), which are equal for an isotropic liquid. -or plots g(r) which is 2 pi r^2 G(r) Berk From: c...@purdue.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_vanhove

[gmx-users] Protein Activity

Hi How can I analyze / describe Protein Activity after MD simulation? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

[gmx-users] Pulling in GROMACS 4.0.3

Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: title= Martini cpp = /usr/bin/cpp integrator

Re: [gmx-users] Pulling in GROMACS 4.0.3

Johnny Lam wrote: Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: By pull apart, do you mean to unwind the secondary structure of the

Re: [gmx-users] Pulling in GROMACS 4.0.3

Hi Justin, Thx for the reply. By pull apart, I just wanted to expose an 'activation site' by using a force. It is somewhat similar to pulling two domains of a protein away from each other. I'm not aiming to undo any secondary structure. I hope this is clearer. Thanks again! --Johnny Johnny

[gmx-users] Max notes = 256 ?

Hi But, I could not compile more than 256 notes when I run the Gromacs. Have anyone experienced compiling more than 1000 notes at one time? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Protein Activity

Hi Lin, Start with defining Protein activity. Tsjerk On Tue, Aug 4, 2009 at 8:11 PM, Chih-Ying Linchihying2...@gmail.com wrote: Hi How can I analyze / describe Protein Activity after MD simulation? Thank you Lin ___ gmx-users mailing

Re: [gmx-users] Pulling in GROMACS 4.0.3

Hi again, I actually figured it out. Turns out, it was a stupid formatting error in the .mdp file. Even though I had it as shown, it didn't read the pull command because it wasn't formatted properly (thought it was still a part of the first line). Sorry guys. --Johnny Hi Justin, Thx for the

Re: [gmx-users] Max notes = 256 ?

Chih-Ying Lin wrote: Hi But, I could not compile more than 256 notes when I run the Gromacs. Have anyone experienced compiling more than 1000 notes at one time? Do you mean nodes? There was a limit of 256 nodes in 3.2 or so, but in 4.0 there is no limit anymore. Thank you Lin

[gmx-users] MD Simulation Errors for Ethylene Glycol-Water System

Hello, I am trying to simulate a simple system of ethylene glycol (ethane-1,2-diol) solvated in a water box. I converted the pdb file to a mol2 file and used topolbuild 1.2.1 to generate topology files: $ topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 I the used

[gmx-users] Check out my photos on Facebook

Hi gmx-users@gromacs.org, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Dmitriy To sign up for Facebook, follow the

Re: [gmx-users] MD Simulation Errors for Ethylene Glycol-Water System

Nancy wrote: Hello, I am trying to simulate a simple system of ethylene glycol (ethane-1,2-diol) solvated in a water box. I converted the pdb file to a mol2 file and used topolbuild 1.2.1 to generate topology files: $ topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff

[gmx-users] topology info for specific bond between atoms in different molecules

Hi There, I am a new user of Gromacs and want to work on carbon nanotubes. I want to simulation carbon nanotube(cnt) bonded with polymers in water. And it will be much better to consider cnt and the bonded polymer as separate molecules, instead of one molecule. I can create the .itp file for

[gmx-users] Regarding the 'hangs at atom 0' issue with x2top 4.x

Hi all, I've recently managed to reproduce the bug with x2top 4.x hanging at atom 0. The halt occurred when I was trying to generate a topology with the -pbc yes option (which is the default used unless you specify otherwise) using a structure file containing no information on the periodic box.

Re: [gmx-users] topology info for specific bond between atoms in different molecules

ucsd mail wrote: Hi There, I am a new user of Gromacs and want to work on carbon nanotubes. I want to simulation carbon nanotube(cnt) bonded with polymers in water. And it will be much better to consider cnt and the bonded polymer as separate molecules, instead of one molecule. I can

Re: [gmx-users] Different force field: Gromacs vs Autodock

Chih-Ying Lin wrote: Hi I use Gromacs (ffG45a3) to run MD in the protein vs ligand system. Then, I use Autodock to calculate the protein-ligand binding energy. As I know the force fields are different between ffG45a3 and Autodock. The two different force fields explain the same system. The

Re: [gmx-users] Max nodes = 256 ?

Chih-Ying Lin wrote: Hi So, which version of Gromacs is more reliable for compiling 1000 nodes now? And, which version with higher computation load per node = computation efficiency? 4.0 4.0.2 4.0.3 4.0.4 If you're making this choice, always use the most up-to-date version of the software

[gmx-users] query regarding ffG43a1bon.itp

Hello I want to add a new bond streching parameter in the ffG43a1bon.itp file, Can anybody please tell me how the values under  Examples of usage in terms of non-bonded atom types'' determined of each bond in the file ffG43a1bon.itp   Subarna Love Cricket? Check out live scores, photos,