Re: [gmx-users] grompp error

On 8/10/2011 12:35 AM, Chunxia Gao wrote: Dear all, I generated the molecule topology from antechamber and then coverted to gromcas topology. When I tried to use grompp first it gave me this error : there is no such molecule type SOL, so I checked the topology file and found out there was n

[gmx-users] snap shot

Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. I don't want to save snap shot for 128 ion-pairs. How can I take average over 128 ion pairs and save snap shot for a single ion pair. Basicall

[gmx-users] order parameter

Hi, I want to calculate order parameter for POPC lipid. After reading the comments made by Justin and Chris about g_order, i would like to compare my results from both g_order and vmd tcl script which will compute order parameters from real hydrogen atoms. Below is the link I found for vmd tc

Re: [gmx-users] Question about Justin's Free Energy Tutorial

I don't think this is a question about new free energy code -- I think this is asking about the fact if you can do a free energy calculation by specifying the A and B variables in the topology, instead of using the MDP coupl-moltype arguments. This is actually the way free energy calculations were

Re: [gmx-users] CHARMM 36 force field

Hi Giovanni, Rather than me just provide you with an mdp file I would suggest that you go through the Klauda paper with a copy of the online GROMACS mdp options open (http://manual.gromacs.org/online/mdp_opt.html). This way you should be able to work out what the appropriate setting are yourse

[gmx-users] grompp error

Dear all, I generated the molecule topology from antechamber and then coverted to gromcas topology. When I tried to use grompp first it gave me this error : there is no such molecule type SOL, so I checked the topology file and found out there was no #include "tip3p.itp" . so I added this to

Re: [gmx-users] (no subject)

Oh, thanks! On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul wrote: > > > Sai Janani Ganesan wrote: > >> Hi, >> >> Thanks for the reply! >> >> I tried the rates, and only the terminal with positive rate gets pulled. >> >> The first and the last amino acids are spatially oriented one behind the >

Re: [gmx-users] Re: atoms jumps from its native position in protein

Parthiban Marimuthu wrote: Hi i am trying to study protein-ligand interaction. at the end of the simulation, the visualization via- VMD shows, some of the atoms suddenly jumped from its place to another space for a short time and comes back to its position connected by huge lines. i dont have

[gmx-users] Re: atoms jumps from its native position in protein

Hi i am trying to study protein-ligand interaction. at the end of the simulation, the visualization via- VMD shows, some of the atoms suddenly jumped from its place to another space for a short time and comes back to its position connected by huge lines. i dont have any idea what is the real techni

[gmx-users] Ligand scattered out of the protein

Dear Sir, I am doing simulation work with protein-ligand complex (3 ligands). I modeled the protein using modeller, their ligand (two) was translated from the template and one them were docked by autodock 4.2. The protein and ligand coordinates were generated as described by the manual. the ligand

[gmx-users] Regarding Density

*Dear All, Please somebody tell me in what way the gromacs calculate the density for given no. of molecules and volume of the box. I generated solvent box using genbox_d command line. Is it right that I can scale the solvent box according to density of my interest after generating box

Re: [gmx-users] 1-week gromacs test at 112x12 cores

2011/10/6 Matthew Zwier > Hi, > > If you don't get any takers, you could always just make a huge box of water > (which usually dominates explicit-solvent MD costs) and run it. That way, > you could scale up the size of the box arbitrarily to achieve good > parallelization across that many cores.