[gmx-users] Lysozyme tutorial-error with moleculetype

Dear Gromacs Users I am doing Justin's Lysozyme tutorial. In EM step I got the error with molecule type. (I am using Gromacs, 4.0.5) It was about Cl and Na. I noticed that because I have selected OPLS forcefield, I should change the name of Cl and Na in my .top file to Na+ and Cl-. I did this

[gmx-users] parameters of a residue

Dear gmx users, Corresponding to your suggestions, I get the parameters for new defined residues from SwissParam. The parameters are not accurate completely. May I face any problem when getting the PMF? and specially for publishing a paper for this reason that the parameters are not accurate as

Re: [gmx-users] constraints between protein ligand - metal chelation

Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like 1 100 6 0.6 1000

[gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] intermolecular H bond selection

Thanks for prompt answering but I may need to clarify my question and sorry for the understanding, For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different dipeptides instead of counting all the possible h bonds between

Re: [gmx-users] restart REMD

Hi Francesco, Thanks! However, it does not work with my case.. tomek On Sun, May 20, 2012 at 1:47 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, usually I use something like: mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* * * gromacs is smart enough to understand

Re: [gmx-users] restart REMD

try put -s before -deffnm mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski tomek.wlodar...@gmail.comwrote: Hi Francesco, Thanks! However, it does not work with my case.. tomek On Sun, May 20, 2012 at 1:47 PM, francesco

[gmx-users] characterising monolayer molecule rotation

Greetings Gromacs, Long time reader, first time poster. I am modelling monolayer/water systems composed of long-chain fatty alcohols and have observed the molecules to rotate around their long-axis, I would like to characterise this using GROMACS. I have had some success calculating the

[gmx-users] LIE methodology check (mdrun -rerun cutoffs and box vectors)

Greetings all, Background: I have a series of MD runs of a protein ligand complex where I have used PME, they represent far more calculations than I have time to repeat in full. I recently became aware that the coulombic interaction energy reported when PME is used is not valid for use with

Re: [gmx-users] intermolecular H bond selection

On Mon, May 21, 2012 at 3:09 AM, mu xiaojia muxiaojia2...@gmail.com wrote: Thanks for prompt answering but I may need to clarify my question and sorry for the understanding, For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different

[gmx-users] Reg trr file

Hello all, I am doing protein-ligand dynamics using GROMACS. i could get all the final files after simulation like gro,edr, log files. But i couldnt get the trr file.Can anyone of you please tell me wht should i do to get this or tell me at what step i have done this mistake. Thank you --