[gmx-users] equilibrium

Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent

Re: [gmx-users] rapid change in the angle of simulation cell - regd

Dear Tsjerk, Thank you for your valuable suggestions, I have done as you have suggested, by doing so my simulation cell has satisfied all the conditions required for the reduced basis lattice but now lattice parameter beta has again changed to 102 degrees which was

[gmx-users] equilibrium

Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of

[gmx-users] kalp-dppc tutoril (Justin tutorials)

Dear Gromacs users, Hello, I want to run the kalp-dppc simulation from Justin tutorials home page.in the step of modifying topology, we see: Make a new directory in your working directory called gromos53a6_lipid.ff and copy the following files from gromos53a6.ff into it: The question: where

Re: [gmx-users] GPU -simulation error -reg

On 10/14/12 8:01 AM, venkatesh s wrote: Respected Gromacs People's, system Containing protein+peptide ( Normally i use the lysosome tutorial md.mdp (only i change the nanosecond) ) mdrun-gpu -v -deffnm md_0_1 while running this i got fatal error like this (Following)

Re: [gmx-users] kalp-dppc tutoril (Justin tutorials)

On 10/14/12 9:12 AM, delara aghaie wrote: Dear Gromacs users, Hello, I want to run the kalp-dppc simulation from Justin tutorials home page.in the step of modifying topology, we see: Make a new directory in your working directory called gromos53a6_lipid.ff and copy the following files from

[gmx-users] equilibrium

Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent

[gmx-users] problem with pull code

Dear Sanku: I don't think that your setup is a particularly good idea. In addition to the potential for rotational problems that you mention, note that the pull force is going to be based on the shortest periodic distance between your group0 and group1. This can be across PBC in the Cartesian

Re: [gmx-users] Lennard-Jones Parameters

Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong

Re: [gmx-users] kalp-dppc tutoril (Justin tutorials)

Hi, Go to GROMACS package in your system, in folder top/share, there you can find force field folders. Sincerely, Shima From: delara aghaie d_agh...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, October 14, 2012 4:42 PM

Re: [gmx-users] Lennard-Jones Parameters

It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to