Re: [gmx-users] Martini Cg-model can not be downloaded!

I just tried ... it is working. XAvier. On Feb 10, 2009, at 8:41 AM, xi zhao wrote: well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model parameters can not be downloaded! Thank you for help! 好

[gmx-users] Martini Cg-model can not be downloaded!

well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model parameters can not be downloaded! Thank you for help! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ h

RE: [gmx-users] shake for water

> Date: Mon, 9 Feb 2009 12:00:52 -0600 > Subject: Re: [gmx-users] shake for water > From: dmob...@gmail.com > To: gmx-users@gromacs.org > > > Hi, > > > > I don't agree. > > It uses the small 1+a approximation for the square. > > Also mdrun prints the rmsd determined with independent code, > > w

[gmx-users] lantibiotics

Hi all, Has anyone tried simulating lantibiotics? The best-known is nisin, but there is a whole family of them. They have a large number of modified amino acids, such as lanthionine (dehydroalanine), methyl-lanthionine, Asp with an extra OH-group attached to the Ca etc., D-alanine, plus sever

Re: [gmx-users] grompp error

Q. Y. HUAN wrote: Dear Justion, I pack the molecules of A, B, ...H together using Packmol (named as md.pdb) then i proceed to pdb2gmx (opls-aa) and editconf. in genbox, I planned to insert another 92 molecules ( T80 ) into the system by edit the .top file. You can notice that i added ""

Re: [gmx-users] grompp error

Dear Justion, I pack the molecules of A, B, ...H together using Packmol (named as md.pdb) then i proceed to pdb2gmx (opls-aa) and editconf. in genbox, I planned to insert another 92 molecules ( T80 ) into the system by edit the .top file. You can notice that i added "" #include "T80.itp" i

[gmx-users] Continuation of Runs and Checkpoint File Use

I just want to check that I have the new behaviour of things right. To start a simulation we have something like: grompp -f md -p KPF -c md_-1 -t md_-1 -e md_-1 -o md_0 mdrun -deffnm md_0 Now, to continue this run once it finishes, for the same length of time specified in the md.mdp file etc, w

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thank you David I would certainly try this way. On Mon, Feb 9, 2009 at 1:08 PM, David Mobley wrote: > Hi, > >> Thanks David, But if I just remove the Copper atom and do the >> simulation as copper is charged there would be sudden change in >> electrostatics and the protein started unfolding when

Re: [gmx-users] grompp error

Q. Y. HUAN wrote: Dear all. I wanted to run grompp in order to perform Em, but it showed me this fatal errer:: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 332520 of the 332520 no

[gmx-users] grompp error

Dear all. I wanted to run grompp in order to perform Em, but it showed me this fatal errer:: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter com

Re: [gmx-users] Pull Peptide Apart

Joseph Johnson wrote: Hello All, I'm fairly new to GROMACS so I apologize for if the question is simple. I have a small peptide that I would like to pull apart. What is the process for doing this? What type of things should I be reading into? Is there any tutorials or code already for such

Re: [gmx-users] how to calculate the viscosity of the bulk

Hi, Berk: I saw your paper about the viscosity calculation method. Can you tell me what exactly I should do using GROMACS to get the fluid viscosity? I used GROMACS-3.3.3 single precision. Thanks a lot in advance. On Tue, Feb 3, 2009 at 1:58 AM, Berk Hess wrote: > Hi, > > This Einstein method of

[gmx-users] Pull Peptide Apart

Hello All, I'm fairly new to GROMACS so I apologize for if the question is simple. I have a small peptide that I would like to pull apart. What is the process for doing this? What type of things should I be reading into? Is there any tutorials or code already for such a process? I've s

Re: [gmx-users] how to calculate the viscosity of the bulk

Dear All: Does anyone knows how to calculate the viscosity of the simulated system except the g_energy -vis. Because I saw some literature that they can get the viscosity but I don't know how.Thanks a lot! On Tue, Feb 3, 2009 at 1:58 AM, Berk Hess wrote: > Hi, > > This Einstein method of g_energ

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Hi, > Thanks David, But if I just remove the Copper atom and do the > simulation as copper is charged there would be sudden change in > electrostatics and the protein started unfolding when I ran the > simulation for 10ns. So I thought perturbing the charge by little > every time I can get a struc

Re: [gmx-users] shake for water

> Hi, > > I don't agree. > It uses the small 1+a approximation for the square. > Also mdrun prints the rmsd determined with independent code, > which is consistent with the (correct) tolerance. Er, yes, I have not turned on SHAKE -- I'm trying to use LINCS for bonds to hydrogen within my molecule

Re: [gmx-users] shake for water

> No, it is not the square. > The code does a small 'a' approximation: (1+a)^2=1+2a+a^2 is approx 1+2a. > I have also tested/benchmark shake in gromacs for my first lincs paper > and the plincs paper and it always behaved the way I thought it would. > > The problem is not that you need more iterati

Re: [gmx-users] shake for water

Berk, > Another question, just to be sure. > Have you actually checked that the other code really gets the distances > right up to 1e-12? Yes. > Berk > >> Date: Thu, 5 Feb 2009 12:03:21 -0600 >> From: dmob...@gmail.com >> To: gmx-users@gromacs.org >> Subject: [gmx-users] shake for water >> >> Al

[gmx-users] gromacs to DLPOLY

Hi gromacs users ! I came across DLPOLY very recently. I am sure some of you might have used both DLPOLY and gromacs. I wanted to know if there are any conversion tools known to you which can convert relevant DLPOLY files to gromacs files. Any help would be appreciated.

Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

Hi Berk, Thanks for your patience. I believe the variable you're talking about corresponds to LAMWORLD in lam/mpi. Even though I wasn't able to make it work, I appreciate your help. Regards, João On Fri, Feb 6, 2009 at 6:01 PM, Berk Hess wrote: > Hi, > > VAR should be an environment variable