[gmx-users] minimization

Dear users I want to minimized a dimer protein but at the first step it start to explosion. I tried to decrease the dt but it is not working. the protein is in the high energy level. Is there any suggestion how to minimized such a high energy level protein?? thanks __

[gmx-users] g_order warning message

Hello, I am trying to use g_order (gmx 4.0.5) on a coarse grained membrane. Because the distances between two atoms two bonds apart is greater than 0.3nm I keep receiving the message: . Warming: distance between atoms * and X > 0.3 nm (**) . Index f

[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,

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] Max nodes = 256 ?

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 Thank you Lin Chih-Ying Lin wrote: > > > > Hi > > But, I could not compile more than 256 notes when I run the

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 tw

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 c

[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

[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 b

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 gmx53

[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

[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 editc

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 ---

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 th

Re: [gmx-users] Protein Activity

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

[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 http://lists.gromacs.org/mailman/listinfo/g

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 > > > Johnn

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 prote

[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

[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 before

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 outpu

[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? Than

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

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 NUMBER,

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 d

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 and

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

[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 outpu

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 correctio

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, 4/8/09,

[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 molecular

[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 Date: 2009/8/4 Subject: help-how to define a new residue in gromacs ? To: tsjerkw HI Tsjerk: can you help me ? My problem is How to define new residue in GROMACS?

Re: [gmx-users] g_wham problem

Oh, that would be convenient.   Thanks.   --- 09年8月3日，周一, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] g_wham problem 收件人: "Discussion list for GROMACS users" 日期: 2009年8月3日,周一,上午9:01 accomp lin wrote: >  Dear all >  Gromacs 3.3.3 seems to have a problem with g_wham and