Re: [gmx-users] POPC Membrane + protein dynamics

Dear, This is the case when you added some ions in your pdb but not define it in your topology, Go in the end of you topology and subtract the number of molecule added. Also define the number of ions added and the name of the ion. like : NA 14 regards, Ravi   

[gmx-users] mean force.

Hi everyone, I use umbrella sample and g_wham to get potential of mean force. However, I also want to compute the mean force. How can I deal with this? Can I get it through calculating the average of data in pullf.xvg file? Thanks in advance. Wende -- ;spring point is equal to r

Re: [gmx-users] Parallel vs Serial Gromacs Run Results

On 27/03/2010 3:57 PM, Sikandar Mashayak wrote: Is there any difference between paralley computed GROMACS results and serially computed results? Yes, but not a significant one. See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation Mark

Re: [gmx-users] Regarding increasing the time period of previous simulation

On 27/03/2010 3:29 PM, sonali dhindwal wrote: Hello All,, I have a query, that I ran my simulation for 1 ns, and now I want to do it further for 2 ns. Then is it possible to carry out my previous simulation to 2 ns from 1 ns, or I have to run it all again ? There's lots of information thoughtfu

[gmx-users] Parallel vs Serial Gromacs Run Results

Is there any difference between paralley computed GROMACS results and serially computed results? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

[gmx-users] Regarding increasing the time period of previous simulation

Hello All,, I have a query, that I ran my simulation for 1 ns, and now I want to do it further for 2 ns. Then is it possible to carry out my previous simulation to 2 ns from 1 ns, or I have to run it all again ? Thanks and Regards -- Sonali Dhindwal The INTERNET now has a personality. Y

Re: [gmx-users] Difference between kinetic energy from .xvg file and calculated kinetic energy from velocities

On 27/03/2010 1:57 PM, Samantha Sanders wrote: Hello! I have run a simulation and using g_energy on the .edr file, I have been looking at the kinetic energies in the resulting .xvg file. It is my understanding that these are the instantaneous kinetic energies for those times. However, when I try

[gmx-users] Difference between kinetic energy from .xvg file and calculated kinetic energy from velocities

Hello! I have run a simulation and using g_energy on the .edr file, I have been looking at the kinetic energies in the resulting .xvg file. It is my understanding that these are the instantaneous kinetic energies for those times. However, when I try to calculate the kinetic energy on

Re: [gmx-users] output forces between group of atoms

On 27/03/2010 8:24 AM, BIN ZHANG wrote: Dear all: In gromacs, is it possible to output forces between two groups of atoms? Yes. Run a trajectory, keep only the frames you wish to analyse, and then use mdrun -rerun on that trajectory with a modified .mdp file. That .mdp file should make suita

[gmx-users] Negative number of RMSD calculations left in g_cluster

Hello everyone, I am attempting to use g_cluster on a large data set (about 69000) frames. I'm on a machine that has 48 GB of RAM, so I shouldn't be running out of memory. As g_cluster runs, it counts down the number of RMSD calculations left. Normally this number is positive (as it should be). Ins

[gmx-users] output forces between group of atoms

Dear all: In gromacs, is it possible to output forces between two groups of atoms? Or is it possible to decompose forces into separate parts, like for LJ, and electrostatics? Thanks, Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] POPC Membrane + protein dynamics

pa...@ncbs.res.in wrote: hi i have tried as per your justin lemkul's tutorial. after aligning the protein with membrane, subsequently we tried to use grompp to generate a tpr file i got the following error. --- Program grompp_mpi, VERSION 3.

Re: [gmx-users] POPC Membrane + protein dynamics

hi i have tried as per your justin lemkul's tutorial. after aligning the protein with membrane, subsequently we tried to use grompp to generate a tpr file i got the following error. --- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.

[gmx-users] Converting SDF to Mol2 Format

Hello All, I need to convert a large number of PubChem SDF files into Mol2 format, for input into Gromacs. I have been using UCSF Chimera to convert an SDF file into Mol2 format; I use Chimera to add partial charges and run energy minimisation on the molecule. So far, I have only been able to co

Re: [gmx-users] Urey Bradley Parameters in GROMACS

PRADEEP VENKATARAMAN wrote: Hello everyone, I have a pdb file of a solvent molecule for which I need to generate a .itp file. The solute is modeled using AMBER and I have topology file generated using amb2gmx.sh. However, the solvent molecule has Urey Bradley parameters specified. Th

[gmx-users] Urey Bradley Parameters in GROMACS

Hello everyone, I have a pdb file of a solvent molecule for which I need to generate a .itp file. The solute is modeled using AMBER and I have topology file generated using amb2gmx.sh. However, the solvent molecule has Urey Bradley parameters specified. Since, I am new to GROMACS I wish to lear

Re: [gmx-users] water box with prescribed volume and density

grivet wrote: Hello Everybody, As a Gromacs newby, I am trying to simulate a box of water (under gromacs4.0.5). I did the following: pdb2gmx -water spce -f spc216.pdb genbox -cs conf.gro -box 5.1 5.1 5.1 -nmol 4412 -o eau270.gro I have the following constraint; I wish to comp

[gmx-users] water box with prescribed volume and density

Hello Everybody, As a Gromacs newby, I am trying to simulate a box of water (under gromacs4.0.5). I did the following: pdb2gmx -water spce -f spc216.pdb genbox -cs conf.gro -box 5.1 5.1 5.1 -nmol 4412 -o eau270.gro I have the following constraint; I wish to compare results with a

Re: [gmx-users] g_helix

Carla Jamous wrote: Hi everyone, Please I need some advice concerning g_helix: It's the first time I use this analysis. In the manual, it says: g helix computes all kind of helix properties. First, _the peptide is checked to find the longest helical part._ This is determined by Hydrogen bond

[gmx-users] g_helix

Hi everyone, Please I need some advice concerning g_helix: It's the first time I use this analysis. In the manual, it says: g helix computes all kind of helix properties. First, *the peptide is checked to find the longest helical part.* This is determined by Hydrogen bonds and Phi/Psi angles. Tha

[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the script below, but it did

Re: [gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

Ozge Engin wrote: Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the

[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the script below, but it did

Re: [gmx-users] what's the differences between double precise version and single precise?

leste 20100326 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080

Re: [gmx-users] g_covar & g_anaeig problems

Hi Jared, Can you post the exact series of commands you used to come to this point, including the selections you used and what constitutes these selections if they are not standard? Please also indicate what was in the trajectory you started off with (xtc-grps). Cheers, Tsjerk On Thu, Mar 25, 2