Re: [gmx-users] Tables - two non-bonded interactions

Hello I think the easiest way to do this is to use multiple tables. Look at: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials There are some details there. ciao Gareth 2011/3/22 Vinícius Contessoto vinicius...@yahoo.com.br: hello! I trying to simulate a protein with

Re: [gmx-users] Tabulated potentials and normal nonbonded interaction at the same time

Hello I think what you need to do is use multiple tables. So you have one table for your CG-solvent interaction with itself and then another one for your CG-solvent (uncharged) interactions. (This second table would then just a tabulated version of the Lennard Jones interaction or whatever you

Re: [gmx-users] Tabulated potentials

Hi I think this is what you need to do: (1) Ensure that the topol.top and index.ndx files are set up in the manner described on the wikki. (2) Put in the mdp file the following: energygrps = A B C energygrp_table = A C B B B C (3) Now create a set of files as follows table.xvg -

Re: [gmx-users] Problem with tabulated potentials for 3 different atoms

Dear Martin As Mark has already told you - if you have a problem with gromacs email the list and wait for a reply. Don't just email people you don't know from Adam and expect them to reply because you are in a rush. The file that you have read from the mailing list contains everything I know

Re: [gmx-users] Topology and force fields

Hello I think what you have been told is wrong. You need to include both ffcharmm27.itp and tip3p.itp as the atomtypes in your tip3p.itp will otherwise not be defined. There is an easy way to check though - take out the include ffcharmm27.itp and try to run grompp on your new topology. My bet

Re: [gmx-users] Potential Tables for user defined potentials

Hi all I have just been stuck on this very problem of user defined potentials. When I emailed this list I was asked if I could make notes on the solution as this is a problem that seems to come up a lot. Anyway, I will send the notes to you separately Sikandar and would ask if anyone knows

Re: Re: [gmx-users] custom forcefields or a new forcefields

Hi Basically you can provide a file in which you calculate the values of your potential function for different values of r. You will have to write a small program to create the table file yourself I think. The details of what should be in it are described in section 6.7.2 of the manual but

Re: Re: [gmx-users] custom forcefields or a new forcefields

Oh almost forgot you also have to put vdw-type = user in the mdp file. As this tell gromacs to read in the tables. Gareth On Thu, Apr 1, 2010 at 3:25 PM, Gareth Tribello gareth.tribe...@gmail.comwrote: Hi Basically you can provide a file in which you calculate the values of your

Re: [gmx-users] Using lennard jones and buckingham terms simultaneously

stands for the charge group. Any help would be greatly appreciated. Gareth On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2010 7:03 AM, Gareth Tribello wrote: Hello again I have tried to do as you suggest and use tables but I have a new problem

Re: [gmx-users] Using lennard jones and buckingham terms simultaneously

Hello again I have tried to do as you suggest and use tables but I have a new problem. First let me describe my process and then you can let me know if there is anything wrong in the stages: OK so first you include the following directives into the mdp file: coulombtype = pme (or whatever

[gmx-users] Using lennard jones and buckingham terms simultaneously

Hello I would like to use gromacs-4 to do a simulation of a small protein in water and in the presence of calcium carbonate. The potential I have for the calcium carbonate uses Buckingham terms for the interaction between the calcium and carbonate ions, while the protein obviously interacts