[gmx-users] g_hbond output analysis

hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns Kindly suggest Parthiban sundar

Re: [gmx-users] g_hbond output analysis

Hi, On Tuesday, 26. August 2008, [EMAIL PROTECTED] wrote: hi i used the -num option for g_hbond run. since i new to gromacs i cannot able to interpret the output form. it comes in 3 columns with the first column indicating the frame, i dont know about the remaining two columns if you use

[gmx-users] Re: Using Morse potentials with ENCAD force field

Using the parameters listed earlier I equalized my system after trying to place the oxygen and nitrogen molecules evenly throughout my system. The result showed the nitrogen molecules fairly even throughout the system but all the oxygen molecules on one side. Any ideas on why the system

[gmx-users] heat_capacity__viscosity

Dear gmx-users, does anybody know some references for C_v(heat cap) and viscosity values for SPCE and the flexible version of SPC water ? For SPC(rigid) , tip4p etc. are lot of literature references but I was not able to find C_v and viscosity for the above mentioned cases... Thank you

[gmx-users] Choose groups for force output

Hi all! From an/during an MD simulation of a protein in water or urea solvent I would like to extract the forces acting on certain protein atoms from the whole solvent (that is, one protein atom but all solvent) at for example every 10th timestep. With nstfout I can set the frequency for

[gmx-users] Genion failing in parallel runs.

Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated: Program

Re: [gmx-users] Genion failing in parallel runs.

Bhanu wrote: Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated:

Re: [gmx-users] Genion failing in parallel runs.

Hi, On Tuesday, 26. August 2008, Bhanu wrote: Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated:

[gmx-users] Re:g_mindist option

Hi I am doing a 5 peptide simulation in a 6nm box. Now to check the correctness of my simulation i m calculating the minimum periodic distance using g_mindist to find out the distance between molecule and its periodic images.Following is the command i have used g_mindist -s full.tpr -f full.xtc

Re: [gmx-users] Re:g_mindist option

[EMAIL PROTECTED] wrote: Hi I am doing a 5 peptide simulation in a 6nm box. Now to check the correctness of my simulation i m calculating the minimum periodic distance using g_mindist to find out the distance between molecule and its periodic images.Following is the command i have used

[gmx-users] Re[2]: Using Morse potentials with ENCAD force field

Could you provide a movie or at least snapshots? What about energy of the system? How it changes? Sorry I am not very good at describing my system. After running the simulation for a while or equilibrating the system all the oxygen molecules move along one wall (a rectangular box

Re: [gmx-users] Re[2]: Using Morse potentials with ENCAD force field

In addition to that information, what parameters are you using for O2? It sounds like something is super attractive within your system, causing the O2 to condense. At what temperature are you simulating? -Justin Vitaly Chaban wrote: Could you provide a movie or at least snapshots? What

[gmx-users] The molecular structure

Hi the molecular structure : bond length, bond angle, dihedral angle the bond length, bond angle are easily determined.. but the dihedral angle are hard to control... with one set of the force field parameter, I could not get the exact structure of the molecule (not all of the dihedral

Re: [gmx-users] The molecular structure

Chih-Ying Lin wrote: Hi the molecular structure : bond length, bond angle, dihedral angle the bond length, bond angle are easily determined.. but the dihedral angle are hard to control... Are you looking to control (i.e., restrain/constrain) these parameters, or measure them?

[gmx-users] Corrupt TRR file -- skipping a bad frame?

I have a corrupt TRR file with a bad frame in the middle; I am wondering if I can remove just the bad frame to utilize all of my good data. To obtain the corrupt TRR file, I first ran a simulation which died (at about 37.9ns) due to a disk quota restriction; this first simulation produced

Re: [gmx-users] Corrupt TRR file -- skipping a bad frame?

Matt Wyczalkowski wrote: I have a corrupt TRR file with a bad frame in the middle; I am wondering if I can remove just the bad frame to utilize all of my good data. To obtain the corrupt TRR file, I first ran a simulation which died (at about 37.9ns) due to a disk quota restriction; this

[gmx-users] g_hbond output analysis

Message: 1 Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST) From: [EMAIL PROTECTED] Subject: [gmx-users] g_hbond output analysis To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=iso-8859-1 hi i used the -num option for g_hbond run. since i new to