[gmx-users] Steepest Descents converged to machine precision

Dear Mark I explain you what I want to ask . I give you a detail of my processing - * step for packing lipid around protein- 1. concatanation of protein and lipid bilayer in proper orientation- I did. 2.Inflate the bilayer by using inflategro script with scaling factor 4 and cutoff 14- I did .

[gmx-users] which structure in NPT MD trjectory should be chosen to start another NVT MD?

Dear gmx users, Usually, we perform NPT MD to achieve optimized density of system and start another NVT MD to calculate other properties of interest. I think there are three possible ways to choose the structure to start another NVT MD:(1) the structure of last step in NPT MD

Re: [gmx-users] Steepest Descents converged to machine precision

nitu sharma wrote: Dear Mark I explain you what I want to ask . I give you a detail of my processing - * step for packing lipid around protein- 1. concatanation of protein and lipid bilayer in proper orientation- I did. 2.Inflate the bilayer by using inflategro script with scaling factor 4

[gmx-users] ffgmx:diffusion of oxygen

Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which matches with that given in the gromacs manual. After equilibrating my system of 1 oxygen and 255 water molecules

Re: [gmx-users] ffgmx:diffusion of oxygen

Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which matches with that given in the gromacs manual. After equilibrating my system of 1 oxygen and

Re: [gmx-users] Steepest Descents converged to machine precision

nitu sharma wrote: Dear mark But how can it possible that starting structure is grossly broken , up to infltegro first step I enquired my structure It looks fine but after doing enegy minimisation step i saw that structure is disturbed OK so what can you deduce from that? It was fine, and

Re: [gmx-users] ffgmx:diffusion of oxygen

Could it be that you have not removed the jumps due to the periodic boudary conditions before using g_msd? Try trjconv -pbc nojump Jochen Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives

[gmx-users] mdrun error

I am trying to run the simulation of protein ligand complex. But after running the mdrun by giving command-grompp –f md. mdp –c pr.gro –p trp.top –o md.tpr and then nohup mdrun –deffnm md the md.log file is showing the following message- Step 11 Warning: pressure scaling more than 1%, mu:

Re: [gmx-users] mdrun error

Pawan Kumar wrote: probably a bad starting structure... check this website for pressure scaling warning : http://wiki.gromacs.org/index.php/Errors Also, compressibility = 4.575e-4 is of the wrong magnitude for water. Should be e-5. -Justin regards, pawan On Mon, Apr 27, 2009

Re: [gmx-users] ffgmx:diffusion of oxygen

Jochen Hub wrote: Could it be that you have not removed the jumps due to the periodic boudary conditions before using g_msd? Try trjconv -pbc nojump Jochen Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule.

Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...

Hi Mark, I tried applying your patch and found some odd installation behavior. We have two systems that I am trying to patch. The first uses gcc-3.3 and worked fine. The other uses gcc-4.2.2, and the compilation failed with: md.c, line 933.18: 1506-046 (S) Syntax error. md.c, line

Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...

Justin A. Lemkul wrote: Hi Mark, I tried applying your patch and found some odd installation behavior. We have two systems that I am trying to patch. The first uses gcc-3.3 and worked fine. The other uses gcc-4.2.2, and the compilation failed with: md.c, line 933.18: 1506-046 (S)

[gmx-users] Resizing membrane (dopc, berger)

Hello dear GROMACS users, Lately I have been trying to user dopc membrane, using Berger united atoms and I am confounded by a problem regarding the size of the membrane. The original membrane from the website is X Y Z (including 128 lipids). Now I would like to multiply the membrane by 1.5

[gmx-users] forcefield for free (neutral) amino acids

Hi all: I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino acids in peptides

RE: [gmx-users] input the .gro and .trr file to the VMD

HI Mark, I am indeed using the coarse-graining atoms .What do you mean by tell VMD to use suitable rules, or something similar. Do you have any fixed case about how to solve this problem in vmd? Thank you very much. Yang From:

Re: [gmx-users] input the .gro and .trr file to the VMD

Best idea is to ask the vmd people, they have their own emailing list. Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a polar transformation On 28/04/2009, at 12:29 PM, He, Yang yang...@mavs.uta.edu wrote: HI Mark, I am indeed using the coarse-graining atoms